ERROR: Assembling failed due to SPAdes failure #251
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I understand the pain of broken SPAdes. However, what you tried is not recommended. Please try to install SPAdes from the source, which should solve the problem. Also, see my replies at #250 |
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Dear JianJun,
Thanks for your reply. Please trust me that I tried many alternatives
without success and followed every issue post. I have spent too much time
on this and at this time it is very frustrating. I can wait until you have
some documentation that explains how to overcome this issue.
Best,
El dom, 26 mar 2023 a las 23:24, JianJun Jin ***@***.***>)
escribió:
… I understand the pain of broken SPAdes. However, what you tried is not
recommended.
Please try to install SPAdes from the source, which should solve the
problem. Also, see my replies at #250
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Natalia Juliana Bayona Vásquez, Ph.D.
Assistant Professor of Biology
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Oxford College
Emory University
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Please update your previous post with a complete log file rather than a truncated one with the running environment removed. |
Kinggerm
changed the title
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You were not offering any running environment information but asking for troubleshooting. It is difficult to help. As I mentioned at #250 , GetOrganelle does not set the version or any other limits on SPAdes. There is no bond here. Solve the SPAdes installation independently from the source and make yourself pass the After you successfully install SPAdes using the source or whatever approach, I can help get GetOrganelle to work with your installed SPAdes. |
I installed the last version of getorganelle: 1.7.7.0, and then it would not work with Spades as many have pointed out. Thus I downloaded the dependencies from the authors (GetOrganelleDep), and what I did was to edit the file 'spades_init.py' within the bin of getorganelle to replace: 'spades_home = abspath(dirname(realpath(file)))' for 'spades_home = 'path_to_/GetOrganelleDep/macOS/SPAdes'. I also change the spades.py path.
When I try to run the test, it runs, but the pre-assembly and assembly fails. Please see below log:
get_organelle_from_reads.py -1 Arabidopsis_simulated.1.fq.gz -2 Arabidopsis_simulated.2.fq.gz -t 1 -o Arabidopsis_simulated.plastome -F embplant_pt -R 10 --overwrite
2023-03-26 06:32:31,652 - INFO: Pre-reading fastq ...
2023-03-26 06:32:31,652 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2023-03-26 06:32:31,752 - INFO: Estimating reads to use finished.
2023-03-26 06:32:31,752 - INFO: Unzipping reads file: Arabidopsis_simulated.1.fq.gz (8796915 bytes)
2023-03-26 06:32:31,863 - INFO: Unzipping reads file: Arabidopsis_simulated.2.fq.gz (9067061 bytes)
2023-03-26 06:32:31,969 - INFO: Counting read qualities ...
2023-03-26 06:32:32,111 - INFO: Identified quality encoding format = Illumina 1.8+
2023-03-26 06:32:32,112 - INFO: Phred offset = 33
2023-03-26 06:32:32,113 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2023-03-26 06:32:32,169 - INFO: Mean error rate = 0.0019
2023-03-26 06:32:32,171 - INFO: Counting read lengths ...
2023-03-26 06:32:32,348 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2023-03-26 06:32:32,348 - INFO: Reads used = 91563+91563
2023-03-26 06:32:32,348 - INFO: Pre-reading fastq finished.
2023-03-26 06:32:32,348 - INFO: Making seed reads ...
2023-03-26 06:32:32,349 - INFO: Seed bowtie2 index existed!
2023-03-26 06:32:32,349 - INFO: Mapping reads to seed bowtie2 index ...
2023-03-26 06:32:42,606 - INFO: Mapping finished.
2023-03-26 06:32:42,606 - INFO: Seed reads made: Arabidopsis_simulated.plastome/seed/embplant_pt.initial.fq (14144302 bytes)
2023-03-26 06:32:42,606 - INFO: Making seed reads finished.
2023-03-26 06:32:42,606 - INFO: Checking seed reads and parameters ...
2023-03-26 06:32:42,606 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2023-03-26 06:32:42,606 - INFO: If the result graph is not a circular organelle genome,
2023-03-26 06:32:42,607 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2023-03-26 06:32:45,467 - INFO: Pre-assembling mapped reads ...
2023-03-26 06:32:45,963 - INFO: Retrying with more reads ..
2023-03-26 06:33:05,013 - WARNING: Pre-assembling failed. The estimations for embplant_pt-hitting base-coverage and word size may be misleading.
2023-03-26 06:33:08,240 - INFO: Estimated embplant_pt-hitting base-coverage = 52.85
2023-03-26 06:33:08,434 - INFO: Estimated word size(s): 98
2023-03-26 06:33:08,434 - INFO: Setting '-w 98'
2023-03-26 06:33:08,434 - INFO: Setting '--max-extending-len inf'
2023-03-26 06:33:08,515 - INFO: Checking seed reads and parameters finished.
2023-03-26 06:33:08,515 - INFO: Making read index ...
2023-03-26 06:33:09,377 - INFO: 178623 candidates in all 183126 reads
2023-03-26 06:33:09,377 - INFO: Pre-grouping reads ...
2023-03-26 06:33:09,377 - INFO: Setting '--pre-w 98'
2023-03-26 06:33:09,391 - INFO: 4074/4074 used/duplicated
2023-03-26 06:33:09,629 - INFO: 517 groups made.
2023-03-26 06:33:09,637 - INFO: Making read index finished.
2023-03-26 06:33:09,637 - INFO: Extending ...
2023-03-26 06:33:09,637 - INFO: Adding initial words ...
2023-03-26 06:33:11,324 - INFO: AW 1113742
2023-03-26 06:33:12,991 - INFO: Round 1: 178623/178623 AI 40378 AW 1126044
2023-03-26 06:33:13,871 - INFO: Round 2: 178623/178623 AI 40411 AW 1126346
2023-03-26 06:33:14,754 - INFO: Round 3: 178623/178623 AI 40411 AW 1126346
2023-03-26 06:33:14,754 - INFO: No more reads found and terminated ...
2023-03-26 06:33:15,065 - INFO: Extending finished.
2023-03-26 06:33:15,066 - INFO: Separating extended fastq file ...
2023-03-26 06:33:15,144 - INFO: Setting '-k 21,55,85,115'
2023-03-26 06:33:15,144 - INFO: Assembling using SPAdes ...
2023-03-26 06:33:15,170 - INFO: spades.py -t 1 --phred-offset 33 -1 Arabidopsis_simulated.plastome/extended_1_paired.fq -2 Arabidopsis_simulated.plastome/extended_2_paired.fq --s1 Arabidopsis_simulated.plastome/extended_1_unpaired.fq --s2 Arabidopsis_simulated.plastome/extended_2_unpaired.fq -k 21,55,85,115 -o Arabidopsis_simulated.plastome/extended_spades
2023-03-26 06:33:15,226 - ERROR: Assembling failed.
Total cost 45.03 s
Thank you!
If then I try to run: spades.py --test, I get:
Traceback (most recent call last):
File "/Users/oxfordlab/anaconda3/envs/getorganelle/bin/spades.py", line 26, in
import support
ModuleNotFoundError: No module named 'support'
Any suggestion? Thanks!
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