add_helixer_workflow #555

rlibouba · 2024-10-08T13:55:29Z

Hello, I would like to propose this workflow in connection with the GTN "Genome annotation with Helixer".
Thank you. Have a nice day!

github-actions · 2024-10-08T14:15:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' --species '' --gff-output-path '/tmp/tmpbjlbttns/job_working_directory/000/2/outputs/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:04:51.802616: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-08 14:04:52.493612: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-08 14:04:57.902564: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:04:58.111355: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:05:00.801827: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:05:03.411030: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:05:06.031928: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat',
 'gff_output_path': '/tmp/tmpbjlbttns/job_working_directory/000/2/outputs/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpufm2it1t
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.24 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.39 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpufm2it1t/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpufm2it1t/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat', 'timestamp': '2024-10-08 14:04:55.157284'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpbjlbttns/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.06 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat in 0.07 hours. GFF file written to /tmp/tmpbjlbttns/job_working_directory/000/2/outputs/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' genomeref.fa &&  gffread '/tmp/tmpbjlbttns/files/8/e/b/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chr_replace	`None`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpbjlbttns/files/8/e/b/dataset_8eba3340-4bd7-48bd-bc95-a30484ee3ef6.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_f1de88e0-4b00-4780-ba4d-165e1945ac11.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpbjlbttns/files/1/8/a/dataset_18a80251-044a-4fd1-a877-53eab06f9e9a.dat' 2>&1 | tail -n +3 >> '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_f1de88e0-4b00-4780-ba4d-165e1945ac11.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_f1de88e0-4b00-4780-ba4d-165e1945ac11.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpbjlbttns/job_working_directory/000/5/outputs/dataset_1cde761f-2623-4b9e-a680-f4aa1cb6f650.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files &&  cp /tmp/tmpbjlbttns/job_working_directory/000/6/configs/tmp4o2spt0x /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files /tmp/tmpbjlbttns/job_working_directory/000/6/configs/tmp4o2spt0x &&  cp /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca_files/index.html /tmp/tmpbjlbttns/job_working_directory/000/6/outputs/dataset_65ce0613-b1cb-415f-a64d-02dd48e287ca.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

busco --in '/tmp/tmpbjlbttns/files/f/f/e/dataset_ffe630b0-92d0-4683-a1e0-1b22062a99d5.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"dad345a4857d11efbde05f6b0006244b"`
chromInfo	`"/tmp/tmpbjlbttns/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - cca0f42c8fe97eb6
- history_state
  - error
- invocation_id
  - cca0f42c8fe97eb6
- invocation_state
  - scheduled
- workflow_id
  - cca0f42c8fe97eb6

github-actions · 2024-10-08T14:41:16Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' --species '' --gff-output-path '/tmp/tmpjo038yv5/job_working_directory/000/2/outputs/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:35:08.583343: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-08 14:35:09.305046: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-08 14:35:14.833701: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:15.087517: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:17.511875: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:19.978380: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:35:22.485818: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat',
 'gff_output_path': '/tmp/tmpjo038yv5/job_working_directory/000/2/outputs/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpb13qee9_
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.25 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.40 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpb13qee9_/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpb13qee9_/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat', 'timestamp': '2024-10-08 14:35:12.001462'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpjo038yv5/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat in 0.07 hours. GFF file written to /tmp/tmpjo038yv5/job_working_directory/000/2/outputs/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:36:49 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-08 14:32:47 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/08/2024 14:32:47 *****
2024-10-08 14:32:47 INFO:	Configuring BUSCO with local environment
2024-10-08 14:32:47 INFO:	Running genome mode
2024-10-08 14:33:01 INFO:	Input file is /tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat
2024-10-08 14:33:01 INFO:	No lineage specified. Running lineage auto selector.

2024-10-08 14:33:01 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-08 14:33:01 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:01 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:01 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-08 14:33:01 INFO:	Running 1 job(s) on bbtools, starting at 10/08/2024 14:33:01
2024-10-08 14:33:02 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-08 14:33:02 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:02 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-08 14:33:02 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:02
2024-10-08 14:33:04 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:04 INFO:	Genetic code 11 selected as optimal
2024-10-08 14:33:04 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:04 INFO:	Running 194 job(s) on hmmsearch, starting at 10/08/2024 14:33:04
2024-10-08 14:33:06 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-08 14:33:07 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-08 14:33:07 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-08 14:33:08 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-08 14:33:09 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-08 14:33:10 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-08 14:33:11 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-08 14:33:12 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-08 14:33:13 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-08 14:33:13 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-08 14:33:13 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-08 14:33:13 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:13 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:14 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-08 14:33:14 INFO:	Skipping BBTools as already run
2024-10-08 14:33:14 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:14 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-08 14:33:14 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:14
2024-10-08 14:33:16 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:16 INFO:	Genetic code 4 selected as optimal
2024-10-08 14:33:16 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:16 INFO:	Running 124 job(s) on hmmsearch, starting at 10/08/2024 14:33:16
2024-10-08 14:33:18 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-08 14:33:19 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-08 14:33:20 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-08 14:33:20 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-08 14:33:21 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-08 14:33:21 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-08 14:33:22 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-08 14:33:22 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-08 14:33:23 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-08 14:33:24 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-08 14:33:24 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-08 14:33:24 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-08 14:33:24 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-08 14:33:24 INFO:	Skipping BBTools as already run
2024-10-08 14:33:24 INFO:	Running 1 job(s) on makeblastdb, starting at 10/08/2024 14:33:24
2024-10-08 14:33:25 INFO:	Creating BLAST database with input file
2024-10-08 14:33:25 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-08 14:33:25 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:33:25 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:33:25
2024-10-08 14:33:26 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:33:26 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:33:26 INFO:	Running Augustus prediction using fly as species:
2024-10-08 14:33:26 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:33:26
2024-10-08 14:33:29 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:33:31 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:33:34 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:33:37 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:33:38 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:33:40 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:33:40 INFO:	Extracting predicted proteins...
2024-10-08 14:33:40 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:40 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:33:40
2024-10-08 14:33:40 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:33:40 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:33:41 INFO:	37 exons in total
2024-10-08 14:33:41 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-08 14:33:41 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-08 14:33:41 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-08 14:33:41 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:33:41 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:33:41
2024-10-08 14:33:51 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:33:51 INFO:	Converting predicted genes to short genbank files
2024-10-08 14:33:51 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/08/2024 14:33:51
2024-10-08 14:33:52 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-08 14:33:52 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-08 14:33:52 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-08 14:33:52 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-08 14:33:52 INFO:	Running 1 job(s) on new_species.pl, starting at 10/08/2024 14:33:52
2024-10-08 14:33:52 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-08 14:33:52 INFO:	Running 1 job(s) on etraining, starting at 10/08/2024 14:33:52
2024-10-08 14:33:53 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-08 14:33:53 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-08 14:33:53 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:33:53 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-08 14:33:53 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:33:53
2024-10-08 14:33:57 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:33:58 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:34:00 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:34:04 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	Extracting predicted proteins...
2024-10-08 14:34:05 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:34:05 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:34:05
2024-10-08 14:34:05 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:34:05 INFO:	37 exons in total
2024-10-08 14:34:05 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-08 14:34:05 INFO:	eukaryota_odb10 selected

2024-10-08 14:34:05 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-08 14:34:05 INFO:	Extract markers...
2024-10-08 14:34:06 INFO:	Place the markers on the reference tree...
2024-10-08 14:34:06 INFO:	Running 1 job(s) on sepp, starting at 10/08/2024 14:34:06
2024-10-08 14:36:46 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-08 14:36:46 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-08 14:36:46 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-08 14:36:46 INFO:	BUSCO analysis done with WARNING(s). Total running time: 225 seconds

***** Summary of warnings: *****
2024-10-08 14:33:01 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:01 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:13 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:13 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:24 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-08 14:36:46 INFO:	Results written in /tmp/tmpjo038yv5/job_working_directory/000/3/working/busco_galaxy
2024-10-08 14:36:46 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-08 14:36:46 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 127 4096 Oct  8 14:34 augustus_output
drwxr-xr-x 3 1001 127 4096 Oct  8 14:33 blast_output
drwxr-xr-x 5 1001 127 4096 Oct  8 14:33 busco_sequences
-rw-r--r-- 1 1001 127 5831 Oct  8 14:34 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Oct  8 14:33 hmmer_output
-rw-r--r-- 1 1001 127 3548 Oct  8 14:34 missing_busco_list.tsv
drwxr-xr-x 2 1001 127 4096 Oct  8 14:36 placement_files
-rw-r--r-- 1 1001 127 3180 Oct  8 14:34 short_summary.json
-rw-r--r-- 1 1001 127 1078 Oct  8 14:34 short_summary.txt
2024-10-08 14:36:47 INFO:	****************** Start plot generation at 10/08/2024 14:36:47 ******************
2024-10-08 14:36:47 INFO:	Load data ...
2024-10-08 14:36:47 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-08 14:36:47 INFO:	Generate the R code ...
2024-10-08 14:36:47 INFO:	Run the R code ...
2024-10-08 14:36:49 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-08 14:36:49 INFO:	Plot generation done. Total running time: 2.2741615772247314 seconds
2024-10-08 14:36:49 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' genomeref.fa &&  gffread '/tmp/tmpjo038yv5/files/e/d/9/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chr_replace	`None`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpjo038yv5/files/e/d/9/dataset_ed96d8a1-c7fe-45f9-b5df-58e9f7431804.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_69b6a85e-92c1-4090-8121-98ab12b4837f.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpjo038yv5/files/b/9/4/dataset_b947ea36-d15a-4beb-bba4-aba284330d6f.dat' 2>&1 | tail -n +3 >> '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_69b6a85e-92c1-4090-8121-98ab12b4837f.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_69b6a85e-92c1-4090-8121-98ab12b4837f.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpjo038yv5/job_working_directory/000/5/outputs/dataset_98d89ef3-b06b-4401-8b96-548b799b1166.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files &&  cp /tmp/tmpjo038yv5/job_working_directory/000/6/configs/tmplvzmfsif /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files /tmp/tmpjo038yv5/job_working_directory/000/6/configs/tmplvzmfsif &&  cp /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770_files/index.html /tmp/tmpjo038yv5/job_working_directory/000/6/outputs/dataset_96b5a021-3e4b-4439-854e-f83500226770.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmpjo038yv5/files/3/b/6/dataset_3b6f8213-9133-4170-8728-7f7fd95294df.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc88760c858111efa0d03d640044c72a"`
chromInfo	`"/tmp/tmpjo038yv5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 70a9d196ab7d53ba
- history_state
  - error
- invocation_id
  - 70a9d196ab7d53ba
- invocation_state
  - scheduled
- workflow_id
  - 70a9d196ab7d53ba

github-actions · 2024-10-08T14:43:00Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' --species '' --gff-output-path '/tmp/tmp88q28s6d/job_working_directory/000/2/outputs/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:36:32.061351: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-08 14:36:32.737547: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-08 14:36:38.160538: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:38.374570: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:40.875694: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:43.349369: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-08 14:36:45.784360: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat',
 'gff_output_path': '/tmp/tmp88q28s6d/job_working_directory/000/2/outputs/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmp6vfv9bei
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.34 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.49 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmp6vfv9bei/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmp6vfv9bei/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat', 'timestamp': '2024-10-08 14:36:35.465286'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp88q28s6d/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat in 0.07 hours. GFF file written to /tmp/tmp88q28s6d/job_working_directory/000/2/outputs/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-08 14:37:23 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-08 14:32:50 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/08/2024 14:32:50 *****
2024-10-08 14:32:50 INFO:	Configuring BUSCO with local environment
2024-10-08 14:32:50 INFO:	Running genome mode
2024-10-08 14:33:10 INFO:	Input file is /tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat
2024-10-08 14:33:10 INFO:	No lineage specified. Running lineage auto selector.

2024-10-08 14:33:10 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-08 14:33:10 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:10 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:10 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-08 14:33:10 INFO:	Running 1 job(s) on bbtools, starting at 10/08/2024 14:33:10
2024-10-08 14:33:12 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-08 14:33:12 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:12 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-08 14:33:12 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:12
2024-10-08 14:33:14 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:14 INFO:	Genetic code 11 selected as optimal
2024-10-08 14:33:14 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:14 INFO:	Running 194 job(s) on hmmsearch, starting at 10/08/2024 14:33:14
2024-10-08 14:33:16 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-08 14:33:18 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-08 14:33:19 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-08 14:33:21 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-08 14:33:22 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-08 14:33:24 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-08 14:33:25 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-08 14:33:27 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-08 14:33:29 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-08 14:33:30 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-08 14:33:30 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-08 14:33:30 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-08 14:33:30 INFO:	Skipping BBTools as already run
2024-10-08 14:33:30 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-08 14:33:30 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-08 14:33:30 INFO:	Running 1 job(s) on prodigal, starting at 10/08/2024 14:33:30
2024-10-08 14:33:33 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-08 14:33:33 INFO:	Genetic code 4 selected as optimal
2024-10-08 14:33:33 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:33:33 INFO:	Running 124 job(s) on hmmsearch, starting at 10/08/2024 14:33:33
2024-10-08 14:33:35 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-08 14:33:36 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-08 14:33:37 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-08 14:33:38 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-08 14:33:39 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-08 14:33:40 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-08 14:33:41 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-08 14:33:42 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-08 14:33:43 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-08 14:33:44 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-08 14:33:44 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-08 14:33:44 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-08 14:33:44 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-08 14:33:44 INFO:	Skipping BBTools as already run
2024-10-08 14:33:44 INFO:	Running 1 job(s) on makeblastdb, starting at 10/08/2024 14:33:44
2024-10-08 14:33:45 INFO:	Creating BLAST database with input file
2024-10-08 14:33:45 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-08 14:33:45 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:33:45 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:33:45
2024-10-08 14:33:47 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:33:47 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:33:47 INFO:	Running Augustus prediction using fly as species:
2024-10-08 14:33:47 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:33:47
2024-10-08 14:33:50 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:33:52 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:33:56 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:33:58 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:33:59 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:34:01 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:34:01 INFO:	Extracting predicted proteins...
2024-10-08 14:34:01 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:34:01 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:34:01
2024-10-08 14:34:02 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:34:02 INFO:	37 exons in total
2024-10-08 14:34:02 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-08 14:34:02 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-08 14:34:02 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-08 14:34:03 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-08 14:34:03 INFO:	Running 1 job(s) on tblastn, starting at 10/08/2024 14:34:03
2024-10-08 14:34:13 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-08 14:34:13 INFO:	Converting predicted genes to short genbank files
2024-10-08 14:34:13 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/08/2024 14:34:13
2024-10-08 14:34:14 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-08 14:34:14 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-08 14:34:14 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-08 14:34:14 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-08 14:34:14 INFO:	Running 1 job(s) on new_species.pl, starting at 10/08/2024 14:34:14
2024-10-08 14:34:14 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-08 14:34:14 INFO:	Running 1 job(s) on etraining, starting at 10/08/2024 14:34:14
2024-10-08 14:34:15 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-08 14:34:15 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-08 14:34:15 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-08 14:34:15 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-08 14:34:15 INFO:	Running 6 job(s) on augustus, starting at 10/08/2024 14:34:15
2024-10-08 14:34:19 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-08 14:34:20 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-08 14:34:21 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-08 14:34:24 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-08 14:34:25 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-08 14:34:26 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-08 14:34:26 INFO:	Extracting predicted proteins...
2024-10-08 14:34:26 INFO:	***** Run HMMER on gene sequences *****
2024-10-08 14:34:26 INFO:	Running 6 job(s) on hmmsearch, starting at 10/08/2024 14:34:26
2024-10-08 14:34:27 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-08 14:34:27 INFO:	37 exons in total
2024-10-08 14:34:27 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-08 14:34:27 INFO:	eukaryota_odb10 selected

2024-10-08 14:34:27 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-08 14:34:28 INFO:	Extract markers...
2024-10-08 14:34:28 INFO:	Place the markers on the reference tree...
2024-10-08 14:34:28 INFO:	Running 1 job(s) on sepp, starting at 10/08/2024 14:34:28
2024-10-08 14:37:19 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-08 14:37:19 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-08 14:37:19 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-08 14:37:19 INFO:	BUSCO analysis done with WARNING(s). Total running time: 249 seconds

***** Summary of warnings: *****
2024-10-08 14:33:10 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:10 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:30 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-08 14:33:44 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-08 14:37:19 INFO:	Results written in /tmp/tmp88q28s6d/job_working_directory/000/3/working/busco_galaxy
2024-10-08 14:37:19 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-08 14:37:19 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 127 4096 Oct  8 14:34 augustus_output
drwxr-xr-x 3 1001 127 4096 Oct  8 14:34 blast_output
drwxr-xr-x 5 1001 127 4096 Oct  8 14:33 busco_sequences
-rw-r--r-- 1 1001 127 5831 Oct  8 14:34 full_table.tsv
drwxr-xr-x 4 1001 127 4096 Oct  8 14:34 hmmer_output
-rw-r--r-- 1 1001 127 3548 Oct  8 14:34 missing_busco_list.tsv
drwxr-xr-x 2 1001 127 4096 Oct  8 14:37 placement_files
-rw-r--r-- 1 1001 127 3180 Oct  8 14:34 short_summary.json
-rw-r--r-- 1 1001 127 1078 Oct  8 14:34 short_summary.txt
2024-10-08 14:37:20 INFO:	****************** Start plot generation at 10/08/2024 14:37:20 ******************
2024-10-08 14:37:20 INFO:	Load data ...
2024-10-08 14:37:20 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-08 14:37:20 INFO:	Generate the R code ...
2024-10-08 14:37:20 INFO:	Run the R code ...
2024-10-08 14:37:23 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-08 14:37:23 INFO:	Plot generation done. Total running time: 2.407008647918701 seconds
2024-10-08 14:37:23 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' genomeref.fa &&  gffread '/tmp/tmp88q28s6d/files/8/9/8/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chr_replace	`None`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmp88q28s6d/files/8/9/8/dataset_898a3f2e-09e0-452d-b752-0c05a730a5df.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_e47c29b1-9042-43f9-b0c0-ea6dcea5d212.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp88q28s6d/files/3/e/b/dataset_3eb29368-f28d-44dc-ae4c-29ed9705e5d9.dat' 2>&1 | tail -n +3 >> '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_e47c29b1-9042-43f9-b0c0-ea6dcea5d212.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_e47c29b1-9042-43f9-b0c0-ea6dcea5d212.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp88q28s6d/job_working_directory/000/5/outputs/dataset_3b701bcd-4d08-45ce-ac5c-5732fafb5ef4.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files &&  cp /tmp/tmp88q28s6d/job_working_directory/000/6/configs/tmplj2vg_1i /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files /tmp/tmp88q28s6d/job_working_directory/000/6/configs/tmplj2vg_1i &&  cp /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98_files/index.html /tmp/tmp88q28s6d/job_working_directory/000/6/outputs/dataset_97c2fa8e-1298-4607-aedf-411af3cf0e98.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmp88q28s6d/files/e/3/a/dataset_e3a07acc-c042-4969-8b1c-a36255f09872.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fc242c7e858111ef99f29be1632487f1"`
chromInfo	`"/tmp/tmp88q28s6d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 49a4bd8b99eb7f47
- history_state
  - error
- invocation_id
  - 49a4bd8b99eb7f47
- invocation_state
  - scheduled
- workflow_id
  - 49a4bd8b99eb7f47

github-actions · 2024-10-10T09:31:57Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' --species '' --gff-output-path '/tmp/tmpcmf3ezyu/job_working_directory/000/2/outputs/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-10 09:24:32.475025: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-10 09:24:33.180938: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-10 09:24:38.730559: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:38.976324: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:41.578172: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:44.176115: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 09:24:46.786359: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat',
 'gff_output_path': '/tmp/tmpcmf3ezyu/job_working_directory/000/2/outputs/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpi3q8kbke
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.24 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.39 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpi3q8kbke/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpi3q8kbke/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat', 'timestamp': '2024-10-10 09:24:35.923143'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpcmf3ezyu/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat in 0.07 hours. GFF file written to /tmp/tmpcmf3ezyu/job_working_directory/000/2/outputs/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-10 09:28:44 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-10 09:23:52 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/10/2024 09:23:52 *****
2024-10-10 09:23:52 INFO:	Configuring BUSCO with local environment
2024-10-10 09:23:52 INFO:	Running genome mode
2024-10-10 09:23:56 INFO:	Input file is /tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat
2024-10-10 09:23:56 INFO:	No lineage specified. Running lineage auto selector.

2024-10-10 09:23:56 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-10 09:23:56 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:23:56 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:23:56 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-10 09:23:56 INFO:	Running 1 job(s) on bbtools, starting at 10/10/2024 09:23:56
2024-10-10 09:23:58 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-10 09:23:58 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 09:23:58 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-10 09:23:58 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 09:23:58
2024-10-10 09:24:01 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 09:24:01 INFO:	Genetic code 11 selected as optimal
2024-10-10 09:24:01 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:24:01 INFO:	Running 194 job(s) on hmmsearch, starting at 10/10/2024 09:24:01
2024-10-10 09:24:05 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-10 09:24:07 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-10 09:24:10 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-10 09:24:13 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-10 09:24:17 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-10 09:24:21 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-10 09:24:24 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-10 09:24:27 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-10 09:24:30 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-10 09:24:33 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-10 09:24:33 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-10 09:24:33 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-10 09:24:33 INFO:	Skipping BBTools as already run
2024-10-10 09:24:33 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 09:24:33 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-10 09:24:33 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 09:24:33
2024-10-10 09:24:36 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 09:24:36 INFO:	Genetic code 4 selected as optimal
2024-10-10 09:24:36 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:24:37 INFO:	Running 124 job(s) on hmmsearch, starting at 10/10/2024 09:24:37
2024-10-10 09:24:39 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-10 09:24:41 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-10 09:24:43 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-10 09:24:45 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-10 09:24:47 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-10 09:24:49 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-10 09:24:51 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-10 09:24:53 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-10 09:24:55 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-10 09:24:57 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-10 09:24:57 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-10 09:24:57 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-10 09:24:57 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-10 09:24:57 INFO:	Skipping BBTools as already run
2024-10-10 09:24:57 INFO:	Running 1 job(s) on makeblastdb, starting at 10/10/2024 09:24:57
2024-10-10 09:24:58 INFO:	Creating BLAST database with input file
2024-10-10 09:24:58 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-10 09:24:58 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 09:24:58 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 09:24:58
2024-10-10 09:25:00 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 09:25:00 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 09:25:00 INFO:	Running Augustus prediction using fly as species:
2024-10-10 09:25:00 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 09:25:00
2024-10-10 09:25:04 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 09:25:06 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 09:25:10 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 09:25:13 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 09:25:15 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 09:25:17 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 09:25:17 INFO:	Extracting predicted proteins...
2024-10-10 09:25:17 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:25:17 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 09:25:17
2024-10-10 09:25:18 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 09:25:18 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 09:25:18 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 09:25:19 INFO:	37 exons in total
2024-10-10 09:25:19 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-10 09:25:19 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-10 09:25:19 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-10 09:25:20 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 09:25:20 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 09:25:20
2024-10-10 09:25:32 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 09:25:32 INFO:	Converting predicted genes to short genbank files
2024-10-10 09:25:32 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/10/2024 09:25:32
2024-10-10 09:25:32 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-10 09:25:32 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-10 09:25:32 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-10 09:25:32 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-10 09:25:32 INFO:	Running 1 job(s) on new_species.pl, starting at 10/10/2024 09:25:32
2024-10-10 09:25:33 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-10 09:25:33 INFO:	Running 1 job(s) on etraining, starting at 10/10/2024 09:25:33
2024-10-10 09:25:34 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-10 09:25:34 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-10 09:25:34 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 09:25:34 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-10 09:25:34 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 09:25:34
2024-10-10 09:25:39 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 09:25:40 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 09:25:42 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 09:25:45 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 09:25:47 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 09:25:48 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 09:25:48 INFO:	Extracting predicted proteins...
2024-10-10 09:25:48 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 09:25:48 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 09:25:48
2024-10-10 09:25:49 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 09:25:49 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 09:25:50 INFO:	37 exons in total
2024-10-10 09:25:50 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-10 09:25:50 INFO:	eukaryota_odb10 selected

2024-10-10 09:25:50 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-10 09:25:50 INFO:	Extract markers...
2024-10-10 09:25:50 INFO:	Place the markers on the reference tree...
2024-10-10 09:25:50 INFO:	Running 1 job(s) on sepp, starting at 10/10/2024 09:25:50
2024-10-10 09:28:39 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-10 09:28:40 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-10 09:28:40 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-10 09:28:40 INFO:	BUSCO analysis done with WARNING(s). Total running time: 284 seconds

***** Summary of warnings: *****
2024-10-10 09:23:56 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:23:56 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:33 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 09:24:57 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-10 09:28:40 INFO:	Results written in /tmp/tmpcmf3ezyu/job_working_directory/000/3/working/busco_galaxy
2024-10-10 09:28:40 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-10 09:28:40 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 118 4096 Oct 10 09:25 augustus_output
drwxr-xr-x 3 1001 118 4096 Oct 10 09:25 blast_output
drwxr-xr-x 5 1001 118 4096 Oct 10 09:24 busco_sequences
-rw-r--r-- 1 1001 118 5831 Oct 10 09:25 full_table.tsv
drwxr-xr-x 4 1001 118 4096 Oct 10 09:25 hmmer_output
-rw-r--r-- 1 1001 118 3548 Oct 10 09:25 missing_busco_list.tsv
drwxr-xr-x 2 1001 118 4096 Oct 10 09:28 placement_files
-rw-r--r-- 1 1001 118 3180 Oct 10 09:25 short_summary.json
-rw-r--r-- 1 1001 118 1078 Oct 10 09:25 short_summary.txt
2024-10-10 09:28:41 INFO:	****************** Start plot generation at 10/10/2024 09:28:41 ******************
2024-10-10 09:28:41 INFO:	Load data ...
2024-10-10 09:28:41 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-10 09:28:41 INFO:	Generate the R code ...
2024-10-10 09:28:41 INFO:	Run the R code ...
2024-10-10 09:28:44 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-10 09:28:44 INFO:	Plot generation done. Total running time: 3.167226552963257 seconds
2024-10-10 09:28:44 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' genomeref.fa &&  gffread '/tmp/tmpcmf3ezyu/files/2/4/d/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chr_replace	`None`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmpcmf3ezyu/files/2/4/d/dataset_24d7c432-03d4-4d92-a83c-0fe657557917.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_260120ec-d58b-4412-b4f3-824af3309cea.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpcmf3ezyu/files/2/0/d/dataset_20de09af-76b1-40e1-b3d2-dc4b783030dc.dat' 2>&1 | tail -n +3 >> '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_260120ec-d58b-4412-b4f3-824af3309cea.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_260120ec-d58b-4412-b4f3-824af3309cea.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpcmf3ezyu/job_working_directory/000/5/outputs/dataset_28df8c72-84fa-457b-9115-852f805cf3c9.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files &&  cp /tmp/tmpcmf3ezyu/job_working_directory/000/6/configs/tmptk4ctt_h /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files /tmp/tmpcmf3ezyu/job_working_directory/000/6/configs/tmptk4ctt_h &&  cp /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5_files/index.html /tmp/tmpcmf3ezyu/job_working_directory/000/6/outputs/dataset_845c8665-0b9d-46e8-ac37-9dc64cdd3bc5.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmpcmf3ezyu/files/c/7/f/dataset_c7f57249-94f9-40c9-87b5-3359bbec2051.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"37203d4686e911efb6217c1e52397065"`
chromInfo	`"/tmp/tmpcmf3ezyu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - ff726b155b645e6d
- history_state
  - error
- invocation_id
  - ff726b155b645e6d
- invocation_state
  - scheduled
- workflow_id
  - ff726b155b645e6d

github-actions · 2024-10-10T17:26:10Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' --species '' --gff-output-path '/tmp/tmp9tr0sopf/job_working_directory/000/2/outputs/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-10 17:16:31.094407: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-10 17:16:31.886043: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-10 17:16:37.746447: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:38.045402: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:40.463150: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:42.768220: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-10 17:16:45.359623: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat',
 'gff_output_path': '/tmp/tmp9tr0sopf/job_working_directory/000/2/outputs/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpp0uh165t
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.25 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.41 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.02 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpp0uh165t/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpp0uh165t/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat', 'timestamp': '2024-10-10 17:16:34.780739'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp9tr0sopf/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.09 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat in 0.07 hours. GFF file written to /tmp/tmp9tr0sopf/job_working_directory/000/2/outputs/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-10 17:20:58 ERROR:	
Warning message:
package ‘ggplot2’ was built under R version 4.4.1 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-10-10 17:16:16 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/10/2024 17:16:16 *****
2024-10-10 17:16:16 INFO:	Configuring BUSCO with local environment
2024-10-10 17:16:16 INFO:	Running genome mode
2024-10-10 17:16:18 INFO:	Input file is /tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat
2024-10-10 17:16:18 INFO:	No lineage specified. Running lineage auto selector.

2024-10-10 17:16:18 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2024-10-10 17:16:18 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:18 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:18 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2024-10-10 17:16:18 INFO:	Running 1 job(s) on bbtools, starting at 10/10/2024 17:16:18
2024-10-10 17:16:19 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-10 17:16:19 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 17:16:19 INFO:	Running Prodigal with genetic code 11 in single mode
2024-10-10 17:16:19 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 17:16:19
2024-10-10 17:16:21 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 17:16:22 INFO:	Genetic code 11 selected as optimal
2024-10-10 17:16:22 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:16:22 INFO:	Running 194 job(s) on hmmsearch, starting at 10/10/2024 17:16:22
2024-10-10 17:16:24 INFO:	[hmmsearch]	20 of 194 task(s) completed
2024-10-10 17:16:25 INFO:	[hmmsearch]	39 of 194 task(s) completed
2024-10-10 17:16:27 INFO:	[hmmsearch]	59 of 194 task(s) completed
2024-10-10 17:16:28 INFO:	[hmmsearch]	78 of 194 task(s) completed
2024-10-10 17:16:30 INFO:	[hmmsearch]	97 of 194 task(s) completed
2024-10-10 17:16:32 INFO:	[hmmsearch]	117 of 194 task(s) completed
2024-10-10 17:16:33 INFO:	[hmmsearch]	136 of 194 task(s) completed
2024-10-10 17:16:35 INFO:	[hmmsearch]	156 of 194 task(s) completed
2024-10-10 17:16:36 INFO:	[hmmsearch]	175 of 194 task(s) completed
2024-10-10 17:16:38 INFO:	[hmmsearch]	194 of 194 task(s) completed
2024-10-10 17:16:38 INFO:	Results:	C:0.5%[S:0.5%,D:0.0%],F:0.0%,M:99.5%,n:194	   

2024-10-10 17:16:38 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2024-10-10 17:16:38 INFO:	Skipping BBTools as already run
2024-10-10 17:16:38 INFO:	***** Run Prodigal on input to predict and extract genes *****
2024-10-10 17:16:38 INFO:	Running Prodigal with genetic code 4 in single mode
2024-10-10 17:16:38 INFO:	Running 1 job(s) on prodigal, starting at 10/10/2024 17:16:38
2024-10-10 17:16:41 INFO:	[prodigal]	1 of 1 task(s) completed
2024-10-10 17:16:41 INFO:	Genetic code 4 selected as optimal
2024-10-10 17:16:41 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:16:41 INFO:	Running 124 job(s) on hmmsearch, starting at 10/10/2024 17:16:41
2024-10-10 17:16:43 INFO:	[hmmsearch]	13 of 124 task(s) completed
2024-10-10 17:16:44 INFO:	[hmmsearch]	25 of 124 task(s) completed
2024-10-10 17:16:45 INFO:	[hmmsearch]	38 of 124 task(s) completed
2024-10-10 17:16:48 INFO:	[hmmsearch]	50 of 124 task(s) completed
2024-10-10 17:17:04 INFO:	[hmmsearch]	63 of 124 task(s) completed
2024-10-10 17:17:09 INFO:	[hmmsearch]	75 of 124 task(s) completed
2024-10-10 17:17:10 INFO:	[hmmsearch]	87 of 124 task(s) completed
2024-10-10 17:17:11 INFO:	[hmmsearch]	100 of 124 task(s) completed
2024-10-10 17:17:12 INFO:	[hmmsearch]	112 of 124 task(s) completed
2024-10-10 17:17:13 INFO:	[hmmsearch]	124 of 124 task(s) completed
2024-10-10 17:17:13 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2024-10-10 17:17:13 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2024-10-10 17:17:13 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2024-10-10 17:17:13 INFO:	Skipping BBTools as already run
2024-10-10 17:17:13 INFO:	Running 1 job(s) on makeblastdb, starting at 10/10/2024 17:17:13
2024-10-10 17:17:14 INFO:	Creating BLAST database with input file
2024-10-10 17:17:14 INFO:	[makeblastdb]	1 of 1 task(s) completed
2024-10-10 17:17:14 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 17:17:14 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 17:17:14
2024-10-10 17:17:16 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 17:17:16 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 17:17:16 INFO:	Running Augustus prediction using fly as species:
2024-10-10 17:17:16 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 17:17:16
2024-10-10 17:17:20 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 17:17:23 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 17:17:27 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 17:17:30 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 17:17:32 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 17:17:34 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 17:17:34 INFO:	Extracting predicted proteins...
2024-10-10 17:17:34 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:17:35 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 17:17:35
2024-10-10 17:17:35 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 17:17:35 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 17:17:35 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 17:17:35 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 17:17:36 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 17:17:36 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 17:17:36 INFO:	37 exons in total
2024-10-10 17:17:36 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2024-10-10 17:17:36 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2024-10-10 17:17:36 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2024-10-10 17:17:36 INFO:	Running a BLAST search for BUSCOs against created database
2024-10-10 17:17:36 INFO:	Running 1 job(s) on tblastn, starting at 10/10/2024 17:17:36
2024-10-10 17:17:48 INFO:	[tblastn]	1 of 1 task(s) completed
2024-10-10 17:17:48 INFO:	Converting predicted genes to short genbank files
2024-10-10 17:17:48 INFO:	Running 3 job(s) on gff2gbSmallDNA.pl, starting at 10/10/2024 17:17:48
2024-10-10 17:17:49 INFO:	[gff2gbSmallDNA.pl]	1 of 3 task(s) completed
2024-10-10 17:17:49 INFO:	[gff2gbSmallDNA.pl]	2 of 3 task(s) completed
2024-10-10 17:17:49 INFO:	[gff2gbSmallDNA.pl]	3 of 3 task(s) completed
2024-10-10 17:17:49 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2024-10-10 17:17:49 INFO:	Running 1 job(s) on new_species.pl, starting at 10/10/2024 17:17:49
2024-10-10 17:17:49 INFO:	[new_species.pl]	1 of 1 task(s) completed
2024-10-10 17:17:49 INFO:	Running 1 job(s) on etraining, starting at 10/10/2024 17:17:49
2024-10-10 17:17:50 INFO:	[etraining]	1 of 1 task(s) completed
2024-10-10 17:17:50 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 252
2024-10-10 17:17:50 INFO:	Running Augustus gene predictor on BLAST search results.
2024-10-10 17:17:50 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2024-10-10 17:17:50 INFO:	Running 6 job(s) on augustus, starting at 10/10/2024 17:17:50
2024-10-10 17:17:55 INFO:	[augustus]	1 of 6 task(s) completed
2024-10-10 17:17:57 INFO:	[augustus]	2 of 6 task(s) completed
2024-10-10 17:17:59 INFO:	[augustus]	3 of 6 task(s) completed
2024-10-10 17:18:02 INFO:	[augustus]	4 of 6 task(s) completed
2024-10-10 17:18:04 INFO:	[augustus]	5 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[augustus]	6 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	Extracting predicted proteins...
2024-10-10 17:18:06 INFO:	***** Run HMMER on gene sequences *****
2024-10-10 17:18:06 INFO:	Running 6 job(s) on hmmsearch, starting at 10/10/2024 17:18:06
2024-10-10 17:18:06 INFO:	[hmmsearch]	1 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	2 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	3 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	4 of 6 task(s) completed
2024-10-10 17:18:06 INFO:	[hmmsearch]	5 of 6 task(s) completed
2024-10-10 17:18:07 INFO:	[hmmsearch]	6 of 6 task(s) completed
2024-10-10 17:18:07 INFO:	37 exons in total
2024-10-10 17:18:07 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255	   

2024-10-10 17:18:07 INFO:	eukaryota_odb10 selected

2024-10-10 17:18:07 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2024-10-10 17:18:07 INFO:	Extract markers...
2024-10-10 17:18:07 INFO:	Place the markers on the reference tree...
2024-10-10 17:18:07 INFO:	Running 1 job(s) on sepp, starting at 10/10/2024 17:18:07
2024-10-10 17:20:53 INFO:	[sepp]	1 of 1 task(s) completed
2024-10-10 17:20:53 INFO:	Not enough markers were placed on the tree (1). Root lineage eukaryota is kept
2024-10-10 17:20:53 INFO:	

    ---------------------------------------------------
    |Results from dataset eukaryota_odb10              |
    ---------------------------------------------------
    |C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:255        |
    |4    Complete BUSCOs (C)                          |
    |4    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |251    Missing BUSCOs (M)                         |
    |255    Total BUSCO groups searched                |
    ---------------------------------------------------
2024-10-10 17:20:53 INFO:	BUSCO analysis done with WARNING(s). Total running time: 276 seconds

***** Summary of warnings: *****
2024-10-10 17:16:18 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:18 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:16:38 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome_prod
2024-10-10 17:17:13 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2024-10-10 17:20:53 INFO:	Results written in /tmp/tmp9tr0sopf/job_working_directory/000/3/working/busco_galaxy
2024-10-10 17:20:53 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-10-10 17:20:53 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwxr-xr-x 8 1001 118 4096 Oct 10 17:18 augustus_output
drwxr-xr-x 3 1001 118 4096 Oct 10 17:17 blast_output
drwxr-xr-x 5 1001 118 4096 Oct 10 17:17 busco_sequences
-rw-r--r-- 1 1001 118 5831 Oct 10 17:18 full_table.tsv
drwxr-xr-x 4 1001 118 4096 Oct 10 17:17 hmmer_output
-rw-r--r-- 1 1001 118 3548 Oct 10 17:18 missing_busco_list.tsv
drwxr-xr-x 2 1001 118 4096 Oct 10 17:20 placement_files
-rw-r--r-- 1 1001 118 3180 Oct 10 17:18 short_summary.json
-rw-r--r-- 1 1001 118 1078 Oct 10 17:18 short_summary.txt
2024-10-10 17:20:55 INFO:	****************** Start plot generation at 10/10/2024 17:20:55 ******************
2024-10-10 17:20:55 INFO:	Load data ...
2024-10-10 17:20:55 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2024-10-10 17:20:55 INFO:	Generate the R code ...
2024-10-10 17:20:55 INFO:	Run the R code ...
2024-10-10 17:20:58 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-10-10 17:20:58 INFO:	Plot generation done. Total running time: 2.808326244354248 seconds
2024-10-10 17:20:58 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' genomeref.fa &&  gffread '/tmp/tmp9tr0sopf/files/9/4/3/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chr_replace	`None`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -s '/tmp/tmp9tr0sopf/files/9/4/3/dataset_94351e8a-63e9-44ac-932f-86e84f76fa16.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_dfdad63d-536e-45fb-90b7-c44715368ff6.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp9tr0sopf/files/6/8/6/dataset_68696577-4bbd-403e-9d45-66006d769a89.dat' 2>&1 | tail -n +3 >> '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_dfdad63d-536e-45fb-90b7-c44715368ff6.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_dfdad63d-536e-45fb-90b7-c44715368ff6.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp9tr0sopf/job_working_directory/000/5/outputs/dataset_780a159f-dd83-4692-9bf6-086b9dc265d4.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir -p /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files &&  cp /tmp/tmp9tr0sopf/job_working_directory/000/6/configs/tmp0vtzdolc /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files /tmp/tmp9tr0sopf/job_working_directory/000/6/configs/tmp0vtzdolc &&  cp /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc_files/index.html /tmp/tmp9tr0sopf/job_working_directory/000/6/outputs/dataset_f3286d92-21ac-44ba-861f-442b3d6dc6fc.dat;

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmp9tr0sopf/files/e/4/1/dataset_e410dcf8-4da1-4afd-a5be-044716cbeadf.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"22602fe6872b11efb621000d3a5c52a4"`
chromInfo	`"/tmp/tmp9tr0sopf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 7a46bb8a29f136d4
- history_state
  - error
- invocation_id
  - 7a46bb8a29f136d4
- invocation_state
  - scheduled
- workflow_id
  - 7a46bb8a29f136d4

github-actions · 2024-10-15T15:38:57Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Galaxy-Workflow-annotation_helixer.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Input:
- step_state: scheduled

Step 2: Helixer:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

/usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' --species '' --gff-output-path '/tmp/tmp7vk7_3fs/job_working_directory/000/2/outputs/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

Exit Code:

```
0
```

Standard Error:

2024-10-15 15:32:16.720998: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-10-15 15:32:17.434596: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-10-15 15:32:22.863717: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:23.114792: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:25.713627: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:28.307060: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2024-10-15 15:32:30.906081: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

Standard Output:

==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat',
 'gff_output_path': '/tmp/tmp7vk7_3fs/job_working_directory/000/2/outputs/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmp07e936s1
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.24 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.39 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmp07e936s1/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmp07e936s1/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat', 'timestamp': '2024-10-15 15:32:20.144514'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp7vk7_3fs/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.07 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat in 0.07 hours. GFF file written to /tmp/tmp7vk7_3fs/job_working_directory/000/2/outputs/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_model	`None`
lineages	`"land_plant"`
option_overlap	`{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}`
post_processing	`{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}`
size	`"8"`
species	`None`
subsequence_length	`None`

Step 3: Busco on genome:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   --augustus   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 4: Gffread:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' genomeref.fa &&  gffread '/tmp/tmp7vk7_3fs/files/d/4/5/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat' -g genomeref.fa      -y pep.fa

Exit Code:

```
0
```

Standard Error:

FASTA index file genomeref.fa.fai created.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chr_replace	`None`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
decode_url	`false`
expose	`false`
filtering	`None`
full_gff_attribute_preservation	`false`
gffs	`{"__current_case__": 0, "gff_fmt": "none"}`
maxintron	`None`
merging	`{"__current_case__": 0, "merge_sel": "none"}`
reference_genome	`{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}`
region	`{"__current_case__": 0, "region_filter": "none"}`

Step 5: Genome annotation statistics:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

ln -s '/tmp/tmp7vk7_3fs/files/d/4/5/dataset_d4560f2f-53d6-4f86-b4f4-186e41de76d3.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_5aefeac5-189f-4b20-b71a-1c09580791b4.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp7vk7_3fs/files/9/3/2/dataset_932b58cc-e381-4dc5-9612-0b6a72de2b2c.dat' 2>&1 | tail -n +3 >> '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_5aefeac5-189f-4b20-b71a-1c09580791b4.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_5aefeac5-189f-4b20-b71a-1c09580791b4.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp7vk7_3fs/job_working_directory/000/5/outputs/dataset_9eea7fe3-531c-4933-8979-e2518f0ce22f.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ref_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`

Step 6: JBrowse:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files &&  cp /tmp/tmp7vk7_3fs/job_working_directory/000/6/configs/tmpn8ghbccm /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files /tmp/tmp7vk7_3fs/job_working_directory/000/6/configs/tmpn8ghbccm &&  cp /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec_files/index.html /tmp/tmp7vk7_3fs/job_working_directory/000/6/outputs/dataset_cde0eabc-0371-4c95-9cb4-e6caf10ef4ec.dat;

Exit Code:

```
0
```

Standard Error:

INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
action	`{"__current_case__": 0, "action_select": "create"}`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gencode	`"1"`
jbgen	`{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}`
plugins	`{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}`
reference_genome	`{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}`
standalone	`"minimal"`
track_groups	[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
uglyTestingHack	`""`

Step 7: Busco on protein:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

busco --in '/tmp/tmp7vk7_3fs/files/2/1/a/dataset_21aa14b6-a430-4119-9915-bf8610175323.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --auto-lineage   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "image", "gff", "missing"]`

Step 8: OMArk:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e81a6a68b0a11efb6217c1e5225427f"`
chromInfo	`"/tmp/tmp7vk7_3fs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"Primates-v2.0.0.h5"`
dbkey	`"?"`
input_iso	`None`
omark_mode	`false`
outputs	`"detail_sum"`
r	`None`
t	`None`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 39f1166267c984e7
- history_state
  - error
- invocation_id
  - 39f1166267c984e7
- invocation_state
  - scheduled
- workflow_id
  - 39f1166267c984e7

add_helixer_workflow

aafd1a4

rlibouba marked this pull request as draft October 8, 2024 13:55

rlibouba added 2 commits October 8, 2024 16:22

fix dockstore error

78f38cf

fix dockstore error

261b7f3

rlibouba added 4 commits October 8, 2024 17:42

modify Galaxy-Workflow-annotation_helixer.ga

081f2c5

fix lint

9abf6e1

typo error

450bfcf

error

351aebd

modify omark

eaa461e

retry

a9c5bf0

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add_helixer_workflow #555

add_helixer_workflow #555

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

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Workflow invocation details

add_helixer_workflow #555

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add_helixer_workflow #555

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Test Summary

Workflow invocation details

github-actions bot commented Oct 8, 2024

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Test Summary

Workflow invocation details

github-actions bot commented Oct 8, 2024

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

github-actions bot commented Oct 10, 2024

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

github-actions bot commented Oct 10, 2024

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

github-actions bot commented Oct 15, 2024

Test Results (powered by Planemo)

Test Summary

Workflow invocation details