Fails on returning empty sequence

[harish0201]

Hi!

Thank you for the wonderful tool! I was testing this out earlier this week and ran into an issue as follows:

INFO [job extract_protein] /tmp/48sbgcsb$ samtools
faidx
--output
output.fasta
--region-file
/tmp/qkhr8fv0/stgf37b22d0-9409-4aeb-ab28-6ba52a517ec7/proteins1.txt
/tmp/qkhr8fv0/stgf94fefbd-b6be-49c5-8ce9-50df72640298/proteins.fasta
samtools: /d/Apps/Miniconda/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /d/Apps/Miniconda/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /d/Apps/Miniconda/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
[W::fai_get_val] Reference W2RFS7 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in W2RFS7
WARNING [job extract_protein] exited with status: 1
WARNING [job extract_protein] completed permanentFail
WARNING [step extract_protein] completed permanentFail
INFO [workflow extract_region_pairs] completed permanentFail
ERROR Workflow cannot make any more progress.
WARNING Final process status is permanentFail
Traceback (most recent call last):
File "/d/Apps/Miniconda/bin/lukasa.py", line 71, in
workflow_output_str = subprocess.check_output(cwl_commandline)
File "/d/Apps/Miniconda/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/d/Apps/Miniconda/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['cwltool', '--no-container', '/d/Apps/Miniconda/share/lukasa/lukasa.cwl', '/tmp/tmp7njg_qgc']' returned non-zero exit status 1.

This is an excerpt from the log. I also extracted the sequences for this particular protein when I ran metaeuk separately, which didn't fail.

Here they are:

W2RFS7|canuscaffold_137_pilon|-|59|5.917e-10|1|7332|7430|7430[7430]:7332[7332]:99[99]
MSKRVPSTLKMDFQNFPVKRGSRSETIATGKPC
W2RFS7|canuscaffold_265_pilon|-|57|2.367e-09|1|3396|3494|3494[3494]:3396[3396]:99[99]
MSNRVPSTLKMDFQNFPVKRGSLSETIANGKPC
W2RFS7|canuscaffold_98_pilon|-|59|5.917e-10|1|7564|7662|7662[7662]:7564[7564]:99[99]
MSKRVPSTLKIDFQNFPVKRGSRSETIATGKPC
W2RFS7|canuscaffold_339_pilon|+|47|2.424e-06|1|114232|114321|114232[114232]:114321[114321]:90[90]
RVPSTLKINFQNFPVKRGSLSEIIATGKPC
W2RFS7|canuscaffold_68_pilon|-|43|3.878e-05|1|13126|13224|13224[13224]:13126[13126]:99[99]
ISIRVPSPLKMDFQNCPVKRGSLSEKIAVGRPC
W2RFS7|canuscaffold_97_pilon|+|57|2.367e-09|1|3248|3346|3248[3248]:3346[3346]:99[99]
MSKRVPSTSKMDFQNFPVKRGSRSETIATGKPC
W2RFS7|canuscaffold_54_pilon|+|58|1.183e-09|1|4187|4285|4187[4187]:4285[4285]:99[99]
MSKRVPSTLKMDFQNFPVKRGSLSETIANGKPC
W2RFS7|canuscaffold_259_pilon|-|48|1.212e-06|1|4997|5083|5083[5083]:4997[4997]:87[87]
VPSTLKMDFQNFPVNRASLSEIIATGKPC
W2RFS7|canuscaffold_115_pilon|-|59|5.917e-10|1|9053|9151|9151[9151]:9053[9053]:99[99]
MSKRVPSTLKIDFQNFPVKRGSRSETIATGKPC
W2RFS7|canuscaffold_319_pilon|-|58|1.183e-09|1|8945|9043|9043[9043]:8945[8945]:99[99]
MSKRVPSTLKMDFQNFPVKRGSLSETIANGKPC
W2RFS7|canuscaffold_210_pilon|+|40|0.0003102|1|7133|7201|7133[7133]:7201[7201]:69[69]
MSKRVPSTLKMDFQNFPVERGSR
W2RFS7|canuscaffold_272_pilon|+|55|9.468e-09|1|5125|5223|5125[5125]:5223[5223]:99[99]
MSKRVPSTLKMDFQNFPLKQGSLSETIANGKPC
W2RFS7|canuscaffold_12_pilon|+|55|9.468e-09|1|57255|57353|57255[57255]:57353[57353]:99[99]
MSKRVPSTLKIDFQNLPVKRGSRSETIANGRPC
W2RFS7|canuscaffold_88_pilon|-|59|5.917e-10|1|19769|19867|19867[19867]:19769[19769]:99[99]
MSKRVPSTLKMDFQNFPVKRGSRSETIATGKPC

The codon sequences:

W2RFS7|canuscaffold_137_pilon|-|59|5.917e-10|1|7332|7430|7430[7430]:7332[7332]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATGGACTTCCAAAACTTCCCAGTGAAGCGAGGGTCTCGGTCAGAGACAATTGCCACAGGCAAGCCGTGT
W2RFS7|canuscaffold_265_pilon|-|57|2.367e-09|1|3396|3494|3494[3494]:3396[3396]:99[99]
ATGTCCAATCGTGTGCCGAGCACCTTGAAGATGGACTTCCAAAACTTCCCAGTGAAGCGAGGATCTCTATCAGAGACAATTGCCAACGGCAAACCGTGT
W2RFS7|canuscaffold_98_pilon|-|59|5.917e-10|1|7564|7662|7662[7662]:7564[7564]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATAGACTTCCAAAACTTCCCAGTGAAGCGAGGGTCTCGGTCAGAGACAATTGCCACGGGCAAACCGTGT
W2RFS7|canuscaffold_339_pilon|+|47|2.424e-06|1|114232|114321|114232[114232]:114321[114321]:90[90]
CGGGTGCCAAGCACCTTGAAGATAAACTTCCAAAACTTTCCCGTGAAGCGAGGATCTCTATCAGAGATAATTGCCACAGGGAAACCGTGT
W2RFS7|canuscaffold_68_pilon|-|43|3.878e-05|1|13126|13224|13224[13224]:13126[13126]:99[99]
ATATCTATTCGGGTGCCAAGCCCGTTGAAGATGGACTTCCAAAATTGCCCCGTGAAGCGAGGATCTCTATCAGAGAAAATTGCGGTAGGCAGACCGTGT
W2RFS7|canuscaffold_97_pilon|+|57|2.367e-09|1|3248|3346|3248[3248]:3346[3346]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTCGAAGATGGACTTCCAAAACTTCCCAGTGAAGCGAGGGTCTCGGTCAGAGACAATTGCCACAGGCAAGCCGTGT
W2RFS7|canuscaffold_54_pilon|+|58|1.183e-09|1|4187|4285|4187[4187]:4285[4285]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATGGATTTCCAAAACTTCCCAGTGAAGCGAGGATCTCTATCAGAGACAATTGCCAACGGCAAACCGTGT
W2RFS7|canuscaffold_259_pilon|-|48|1.212e-06|1|4997|5083|5083[5083]:4997[4997]:87[87]
GTGCCAAGCACCTTGAAGATGGACTTCCAAAACTTTCCAGTGAATCGAGCATCTCTATCAGAGATAATTGCGACAGGAAAACCGTGT
W2RFS7|canuscaffold_115_pilon|-|59|5.917e-10|1|9053|9151|9151[9151]:9053[9053]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATAGACTTCCAAAACTTCCCAGTGAAGCGAGGGTCTCGGTCAGAGACAATTGCCACGGGCAAACCGTGT
W2RFS7|canuscaffold_319_pilon|-|58|1.183e-09|1|8945|9043|9043[9043]:8945[8945]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATGGACTTCCAAAACTTCCCAGTGAAGCGAGGATCTCTATCAGAGACAATTGCCAACGGCAAACCGTGT
W2RFS7|canuscaffold_210_pilon|+|40|0.0003102|1|7133|7201|7133[7133]:7201[7201]:69[69]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATGGATTTCCAAAACTTCCCAGTAGAGCGAGGATCTCGA
W2RFS7|canuscaffold_272_pilon|+|55|9.468e-09|1|5125|5223|5125[5125]:5223[5223]:99[99]
ATGTCCAAACGTGTGCCGAGCACATTGAAGATGGACTTCCAAAACTTCCCACTGAAGCAAGGATCTCTATCAGAGACAATTGCCAACGGCAAACCGTGT
W2RFS7|canuscaffold_12_pilon|+|55|9.468e-09|1|57255|57353|57255[57255]:57353[57353]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATAGACTTCCAAAACTTACCAGTGAAGCGGGGATCTCGATCAGAGACAATTGCCAACGGCAGACCGTGT
W2RFS7|canuscaffold_88_pilon|-|59|5.917e-10|1|19769|19867|19867[19867]:19769[19769]:99[99]
ATGTCCAAACGTGTGCCGAGCACCTTGAAGATGGACTTCCAAAACTTCCCAGTGAAGCGAGGGTCTCGGTCAGAGACAATTGCCACAGGCAAGCCGTGT

I'm not sure where the issue is, because it stops here randomly. I can send the protein and contig fasta if needed.

[harish0201]

Ah, got this fixed probably. My protein sequence headers were of the format:

>tr|protein|protein_species

fasta headers were:
>canuscaffold_1_pilon

Modifying the two to:
>protein_species or >protein
>canuscaffold_1

Now it seems to run without a hitch.

[pvanheus]

Thanks for the report @harish0201. I think I know where the problem is coming from - it parses the sequence header to extract MetaEuk alignment information.

I am currently quite actively developing the tool so I will try and fix this bug in a future release.