[iqbal-lab/Mykrobe-predictor] IndexError: list index out of range exception on Linux but not Mac (#126)

[ponomarevsy]

(mykrobeenv) [appbuild@ai-submit1]» pip freeze
biopython==1.70
easybuild-easyblocks==2.9.0
easybuild-easyconfigs==2.9.0
easybuild-framework==2.9.0
future==0.16.0
ga4ghmongo==0.0.1.2
mongoengine==0.13.0
mykatlas==0.6.1
mykrobe==0.5.6
numpy==1.13.1
pymongo==3.4.0
PyVCF==0.6.8
six==1.10.0
vsc-base==2.5.4
vsc-install==0.10.15

Dear Mykrobe-predictor support team:

I have recompiled mccortex31 and copied the executable under mykrobe’s bin folder. Sadly, “mykrobe predict” still fails. I wonder if “mykatlas==0.6.1” is an incorrect version. Will wait for comments from Phelim Bradley (please forward his reply to me). Thanks!

» mccortex31 --version
Error: Unrecognised command: --version
usage: mccortex31 [options]
version: mccortex=v0.0.3-482-g22410ea zlib=1.2.8 htslib=1.2.1-250-gfa6ed9a ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31

Commands: breakpoints use a trusted assembled genome to call large events
bubbles find bubbles in graph which are potential variants
build construct cortex graph from FASTA/FASTQ/BAM
calls2vcf convert bubble/breakpoint calls to VCF
check load and check graph (.ctx) and path (.ctp) files
clean clean errors from a graph
contigs assemble contigs for a sample
correct error correct reads
coverage print contig coverage
dist make colour kmer distance matrix
index index a sorted cortex graph file
inferedges infer graph edges between kmers before calling thread
join combine graphs, filter graph intersections
links clean and plot link files (.ctp)
pjoin merge path files (.ctp)
popbubbles pop bubbles in the population graph
pview text view of a cortex path file (.ctp)
reads filter reads against a graph
rmsubstr reduce set of strings to remove substrings
server interactively query the graph
sort sort the kmers in a graph file
subgraph filter a subgraph using seed kmers
thread thread reads through cleaned graph to make links
uniqkmers generate random unique kmers
unitigs pull out unitigs in FASTA, DOT or GFA format
vcfcov coverage of a VCF against cortex graphs
vcfgeno genotype a VCF after running vcfcov
view text view of a cortex graph file (.ctx)

Type a command with no arguments to see help.

Common Options:
-h, --help Help message
-q, --quiet Silence status output normally printed to STDERR
-f, --force Overwrite output files if they already exist
-m, --memory Memory e.g. 1GB [default: 1GB]
-n, --nkmers Hash entries [default: 4M, ~4 million]
-t, --threads Limit on proccessing threads [default: 2]
-o, --out Output file
-p, --paths <in.ctp> Links file to load (can specify multiple times)

(mykrobeenv) appbuild@ai-submit1» module show mykrobe

/sysapps/cluster/modules/all/mykrobe/0.5.6-Python-3.5:

module-whatis Description: Mykrobe Predictor analyses the whole genome of a bacterial sample, all within a couple of minutes, and predicts which drugs the infection is resistant to. - Homepage: https://github.com/iqbal-lab/Mykrobe-predictor
conflict mykrobe
prepend-path CPATH /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/include
prepend-path LD_LIBRARY_PATH /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/lib
prepend-path LIBRARY_PATH /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/lib
prepend-path MANPATH /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/share/man
prepend-path PATH /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/bin
prepend-path PKG_CONFIG_PATH /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/lib/pkgconfig
setenv EBROOTGEMINI /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv
setenv EBVERSIONGEMINI 0.5.6
prepend-path PATH /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv

(mykrobeenv) appbuild@ai-submit1» ls /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/bin
2to3 easy_install mykrobe pydoc3.5 python3-config vcf_melt
2to3-3.5 easy_install-3.5 openssl python pyvenv vcf_sample_filter.py
activate f2py pasteurize python3 pyvenv-3.5 wheel
atlas futurize pip python3.5 sqlite3 wish8.5
conda idle3 pycache python3.5-config tclsh8.5 xz
c_rehash idle3.5 pydoc python3.5m unxz
deactivate mccortex31 pydoc3 python3.5m-config vcf_filter.py

(mykrobeenv) appbuild@ai-submit1» which mccortex31
~/eb_files/Mykrobe-predictor/Mykrobe-predictor/mccortex/bin/mccortex31

(mykrobeenv) appbuild@ai-submit1» cp ~/eb_files/Mykrobe-predictor/Mykrobe-predictor/mccortex/bin/mccortex31 /sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/bin/.

(mykrobeenv) appbuild@ai-submit1» mykrobe predict SRR5486866 tb --seq /hpcdata/bcbb/tbportal/genomics/SequencingCenterDownloads/Borstel/Romania_50samples/TBprofiler/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/mykrobeenv/bin/mykrobe", line 11, in
sys.exit(main())
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/lib/python3.5/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/mykrobeenv/lib/python3.5/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/mykrobeenv/lib/python3.5/site-packages/mykrobe/cmds/amr.py", line 134, in run
cp.run()
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/lib/python3.5/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/mykrobeenv/lib/python3.5/site-packages/mykatlas/typing/typer/genotyper.py", line 128, in _parse_covgs
row)
File "/sysapps/cluster/software/Anaconda/2.3.0Linux-x86_64/envs/mykrobeenv/lib/python3.5/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

[ponomarevsy]

A quick update: this somehow fixed itself... Most likely, there was not enough disk space to process the file and/or the path to the FASTA file was incorrect.