IndexError-list index out of range

[buihoangphuc412]

I ran this command annotate_hits_pyseer significant_kmers_amox.txt references.txt annotated_kmers_amox.txt and get error: 100 kmers remain Reference 1 [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -v 1 -k 8 CHC97.fasta /media/sf_Biolinux/Antibiotic project/pyseer/remaining_kmers.fa [main] Real time: 0.125 sec; CPU: 0.114 sec Traceback (most recent call last): File "/home/manager/miniconda3/envs/test/bin/annotate_hits_pyseer", line 10, in sys.exit(main()) File "/home/manager/miniconda3/envs/test/lib/python3.7/site-packages/pyseer/kmer_mapping/annotate_hits.py", line 179, in main up_genes = extract_genes(sorted_query.closest(b=ref_annotation, s=False, D="ref", iu=True, stream=True)) File "/home/manager/miniconda3/envs/test/lib/python3.7/site-packages/pyseer/kmer_mapping/annotate_hits.py", line 52, in extract_genes for tag in match.fields[15].split(";"): IndexError: list index out of range

I attached files for running references.txt significant_kmers_amox.txt

[johnlees]

@mgalardini The range error seems common in this script, whenever bwa gives something with surprising formatting. Maybe we should put it in a try/catch?

[mgalardini]

Agreed! Will try to implement something in the next couple of days, we are due a new version as well I think

[mgalardini]

@buihoangphuc412 would you mind sharing the fasta and gff file for sample CHC97?

Thanks

[buihoangphuc412]

I attached the files. Thanks

Vào Th 3, 27 thg 4, 2021 vào lúc 19:14 Marco Galardini < @.***> đã viết:

@buihoangphuc412 https://github.com/buihoangphuc412 would you mind sharing the fasta and gff file for sample CHC97?

Thanks

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[mgalardini]

Sorry, I don't see them, you may need to attach them by replying to the message using Github's interface

[buihoangphuc412]

CHC97.zip

[mgalardini]

Which version of pyseer are you using? I can't reproduce the error using pyseer v1.3.4 or from the latest commit

[buihoangphuc412]

I used the new version pyseer --version pyseer 1.3.6

[mgalardini]

Tried that too, but I'm not encountering any error. Let's make sure we have no other version mismatch; here's the version of the other relevant libraries/software:

• python 3.9.2
• pybedtools 0.8.2
• bwa 0.7.17-r1188

My output (truncated before it fails because I don't have the other references):

~/workspace/pyseer/issue_145$ annotate_hits_pyseer significant_kmers_amox.txt references.txt output
100 kmers remain                                                                                         
Reference 1                                                                                              
[main] Version: 0.7.17-r1188                                                                             
[main] CMD: bwa mem -v 1 -k 8 CHC97.fasta /home/m/workspace/pyseer/issue_145/remaining_kmers.fa
[main] Real time: 0.060 sec; CPU: 0.061 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs                                                                                                                                                                     
[main] Version: 0.7.17-r1188
[main] CMD: bwa fastmap -w 100 -l 9 CHC97.fasta /home/m/workspace/pyseer/issue_145/remaining_kmers.fa
[main] Real time: 0.008 sec; CPU: 0.010 sec                                                              
71 kmers remain
Draft reference 2

[mgalardini]

Closing for lack of follow-up replies and could not reproduce