iqbal-lab/Mykrobe-predictor

IndexError: list index out of range exception on Linux but not Mac

Closed this issue · 9 comments

harrismia commented

Hello,

    I am getting the error message:   IndexError: list index out of range when I try to run mykrobe predict on our linux environment.   When I run it on my Mac Book Pro it works fine.  The error message is below: 

    Any ideas about why this is happening?   Thanks in advance!

mykrobe predict SRR5486866 tb --seq ./SRR5486866_1.fastq.gz
INFO:root:Running AMR prediction with panels data/panels/tb-species-170421.fasta.gz, data/panels/tb-walker-probe-set-feb-09-2017.fasta.gz
Traceback (most recent call last):
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/bin/mykrobe", line 11, in
sys.exit(main())
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 125, in main
args.func(parser, args)
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 34, in run_subtool
run(parser, args)
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykrobe/cmds/amr.py", line 134, in run
cp.run()
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 74, in run
self._parse_covgs()
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 128, in _parse_covgs
row)
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 118, in _parse_summary_covgs_row
return row[0], int(row[2]), int(row[3]), 100 * float(row[4]), int(row[5])
IndexError: list index out of range

iqbal-lab commented

What precise version of predictor are you using - did you get it from github? Do you have a commit number? How did you install , and has it worked for you before?

harrismia commented

Hi,

We did get if from github. For the linux version: typing mykrobe --version gives : mykrobe v0.5.6-0-gbd7923a-dirty

The same command on my Mac Book Pro gives: mykrobe v0.5.1-0-g04fef92 I see that they are different. I have been using the version on my Mac Book but we have never tried using it on our linux cluster before.

I didn't do the install on the linux cluster so I will find out the details and respond. Thanks,
Michael

Phelimb commented

@harrismia Could you upload the output of pip freeze when run within your virtualenv ? This looks like the version of mykatlas is incompatible with the version of mykrobe.

Phelimb commented

It looks like the local install of mccortex seems to fail with anaconda venvs. You might need to reinstall mccortex.

	git clone --recursive https://github.com/iqbal-lab/Mykrobe-predictor.git
	cd Mykrobe-predictor
	cd mccortex
	make    
	export PATH=$(pwd)/bin:$PATH
	cd ..

The version should read:

mccortex31 --version 
mccortex=v0.0.3-482-g22410ea
harrismia commented
iqbal-lab commented

I'm just going on holiday, so will ping @Phelimb

noporpoise commented

Looks like Mykrobe-predictor should be using the McCortex vcfgeno command instead of geno.

Phelimb commented

So, I have a branch of mccortex where geno is a valid command that should work with Mykrobe predictor.

https://github.com/phelimb/mccortex/tree/genotype

I'm not 100% sure what's causing this error but it seems to be a version clash between mccortex, or mykaltlas.

You have the correct mykatlas but the mccortex version should be v0.0.3-481-gbbe4edf-dirty

Which you can get manually by running

git clone -b genotype https://github.com/phelimb/mccortex

joshualoving commented

When I compile https://github.com/phelimb/mccortex/tree/genotype, I get the same version number mccortex=v0.0.3-482-g22410ea, not v0.0.3-481-gbbe4edf-dirty