KeyError:530 when running the pipeline

[harrismia]

Hi Jody,

I am getting the following error when I run the pipline on one of our files.   I am using version 2.6.   It is working on most of our files but fails on this one for some reason.  Unfortunately I am not able to share the file at this time.  

Thanks, 


   Michael 

Running command:
set -u pipefail; samtools view -bL /sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/share/tbprofiler/tbdb.bed bamDir/fileWerror.bam | samtools depth -aa --reference /sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/share/tbprofiler/tbdb.fasta -
Traceback (most recent call last):
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3//bin/tb-profiler", line 347, in
args.func(args)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3//bin/tb-profiler", line 93, in main_profile
results = tbp.reformat(results,conf)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/lib/python3.7/site-packages/tbprofiler/reformat.py", line 247, in reformat
results = reformat_annotations(results,conf)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/lib/python3.7/site-packages/tbprofiler/reformat.py", line 217, in reformat_annotations
var["change"] = pp.reformat_mutations(var["change"],var["type"],var["locus_tag"],chr2gene_pos)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/lib/python3.7/site-packages/pathogenprofiler/utils.py", line 53, in reformat_mutations
gene_start = gene_info[chr_pos] + 1
KeyError: 530

[jodyphelan]

I had found some similar looking error messages and have uploaded a fix with the latest pathogen-profiler commit. Try updating this library and check if you still get the error.

Jody

[harrismia]

Unfortunately, I am still getting the error (see below). This is on a different file than the original bug report. I am getting KeyError: 1290

I do have file that I can share with you for debugging purposes. What would be the best way to get it to you? It is not yet in a public repository.

set -u pipefail; samtools view -bL /sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/share/tbprofiler/tbdb.bed S132.bam | samtools depth -aa --reference /sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/share/tbprofiler/tbdb.fasta -
Traceback (most recent call last):
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3//bin/tb-profiler", line 347, in
args.func(args)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3//bin/tb-profiler", line 93, in main_profile
results = tbp.reformat(results,conf)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/lib/python3.7/site-packages/tbprofiler/reformat.py", line 247, in reformat
results = reformat_annotations(results,conf)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/lib/python3.7/site-packages/tbprofiler/reformat.py", line 217, in reformat_annotations
var["change"] = pp.reformat_mutations(var["change"],var["type"],var["locus_tag"],chr2gene_pos)
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-2.6-python3/lib/python3.7/site-packages/pathogenprofiler/utils.py", line 69, in reformat_mutations
gene_start = gene_info[chr_pos]
KeyError: 1290

[harrismia]

Hi Jody,

I saw that you sent me a response to this with instructions on where to put the file but I can't seem to find it. Could you send it again? Thanks.

[jodyphelan]

Just sent it again.

[jodyphelan]

This issue is now fixed in the latest conda build (v2.6.1)

[harrismia]

Thanks a lot! We will update to version 2.6.1 and let you know if we run into any issues.