Flight error.

[Valentin-Bio]

Hello iI ran rosella over my paired end metagneomic sequencing data as the following:

rosella recover -r assembly/final.contigs.fa -1 R1 -2 R2 -o rosella_bins --threads 12

On my output directory I have rosella_coverages.tsv and rosella_kmer_table.tsv files

but looking to my log file, it seems that flight failed:

[2023-01-24T11:27:52Z INFO rosella] rosella version 0.4.2
[2023-01-24T11:27:52Z INFO rosella] Using min-covered-fraction 0%
[2023-01-24T11:27:52Z INFO rosella] Using min-read-aligned-percent 0%
[2023-01-24T11:27:52Z INFO coverm::mapping_index_maintenance] Generating MINIMAP2_SR index for assembly/final.contigs.fa ..
[2023-01-24T11:28:12Z INFO coverm::mapping_index_maintenance] Finished generating MINIMAP2_SR index.
[2023-01-24T11:28:14Z INFO rosella::estimation::contig] Processing short reads...
[2023-01-29T06:14:19Z ERROR bird_tool_utils::command] Error when running flight process. Exitstatus was : ExitStatus(unix_wait_status(256))
thread 'main' panicked at 'Failed to grab stderr from failed flight process', /home/conda/.cargo/registry/src/github.com-1ecc6299db9ec823/bird_tool_utils-0.3.0/src/command.rs:17:14
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

testing if flight was available I ran

flight --help

but I got another error message:

Traceback (most recent call last):
File "/home/toshiba/miniconda3/envs/rosella/bin/flight", line 5, in
from flight.flight import main
File "/home/toshiba/miniconda3/envs/rosella/lib/python3.10/site-packages/flight/flight.py", line 22, in
from Bio import SeqIO
File "/home/toshiba/.local/lib/python3.10/site-packages/Bio/SeqIO/init.py", line 374, in
from Bio.Align import MultipleSeqAlignment
File "/home/toshiba/.local/lib/python3.10/site-packages/Bio/Align/init.py", line 35, in
from Bio.Align import substitution_matrices
File "/home/toshiba/.local/lib/python3.10/site-packages/Bio/Align/substitution_matrices/init.py", line 15, in
class Array(numpy.ndarray):
AttributeError: module 'numpy' has no attribute 'ndarray'

[rhysnewell]

Interesting, looks like an error originating from the Biopython package using deprecated numpy features or maybe just a corrupted install. Have you tried:

pip uninstall Biopython
pip uninstall numpy
pip install Biopython
flight --help

[rhysnewell]

If this did not fix, then there may be a strange dependency issue with skbio so if you have any other errors pop up please post them here

[Valentin-Bio]

Hello, yes my server is down these days, I will give a try with your suggestions soon.

Thanks

[rhysnewell]

Hi @Valentin-Bio , Apologies for the delay I've been swamped but had some inspiration this weekend. v0.5.0 should fix this issue if you create a new conda environment and install from the bioconda channel. If you still get an error from flight, please open a new issue and post the error log that gets produced. The flight error should be exposed to users now.