[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 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.