"mccortex geno" invalid command

[RaSieb]

possibly related to #126 : I installed Mykrobe on linux using pip, and mccortex separately using clone and make. mccortex runs when tested alone, and is in PATH. Running mykrobe, however, returns an error where mykrobe tries to run a command "mccortex31 geno [...]" which is not recognised by mccortex.

Error message: mykrobe predict test2 staph --mccortex31_path /srv/data/AS/RASI/Mykrobe/mccortex/bin/mccortex31 -1 55-100-060*.gz INFO:root:Running AMR prediction with panels data/panels/staph-species-160227.fasta.gz, data/panels/staph-amr-bradley_2015-feb-17-2017.fasta.gz DEBUG:mykatlas.cortex.mccortex:running /srv/data/AS/RASI/Mykrobe/mccortex/bin/mccortex31 geno -q -t 1 -m 1GB -k 15 -o /tmp//test2-15_staph-species-160227-staph-amr-bradley_2015-feb-17-2017.covgs -I /tools/linuxbrew/lib/python3.6/site-packages/mykatlas/atlas/data/skeletons/staph-species-160227-staph-amr-bradley_2015-feb-17-2017_15.ctx -s test2-15 -1 55-100-060_R1.fastq.gz -1 55-100-060_R2.fastq.gz -c /tools/linuxbrew/lib/python3.6/site-packages/mykrobe/data/panels/staph-species-160227.fasta.gz -c /tools/linuxbrew/lib/python3.6/site-packages/mykrobe/data/panels/staph-amr-bradley_2015-feb-17-2017.fasta.gz /tmp//test2-15_staph-species-160227-staph-amr-bradley_2015-feb-17-2017.ctx Error: Unrecognised command: geno usage: mccortex31 [options] version: mccortex=v0.0.3-554-ga7d6f3b zlib=1.2.11 htslib=1.3.2-208-gd8d0323 ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31

[usage removed]

Traceback (most recent call last): File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykatlas/cortex/mccortex.py", line 210, in _run_coverage_if_required subprocess.check_output(self.coverages_cmd) File "/tools/linuxbrew/opt/python3/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/tools/linuxbrew/opt/python3/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/srv/data/AS/RASI/Mykrobe/mccortex/bin/mccortex31', 'geno', '-q', '-t', '1', '-m 1GB', '-k', '15', '-o', '/tmp//test2-15_staph-species-160227-staph-amr-bradley_2015-feb-17-2017.covgs', '-I', '/tools/linuxbrew/lib/python3.6/site-packages/mykatlas/atlas/data/skeletons/staph-species-160227-staph-amr-bradley_2015-feb-17-2017_15.ctx', '-s', 'test2-15', '-1', '55-100-060_R1.fastq.gz', '-1', '55-100-060_R2.fastq.gz', '-c', '/tools/linuxbrew/lib/python3.6/site-packages/mykrobe/data/panels/staph-species-160227.fasta.gz', '-c', '/tools/linuxbrew/lib/python3.6/site-packages/mykrobe/data/panels/staph-amr-bradley_2015-feb-17-2017.fasta.gz', '/tmp//test2-15_staph-species-160227-staph-amr-bradley_2015-feb-17-2017.ctx']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/tools/linuxbrew/bin/mykrobe", line 11, in sys.exit(main()) File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykrobe/mykrobe_predictor.py", line 125, in main args.func(parser, args) File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykrobe/mykrobe_predictor.py", line 34, in run_subtool run(parser, args) File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykrobe/cmds/amr.py", line 134, in run cp.run() File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykatlas/typing/typer/genotyper.py", line 73, in run self._run_cortex() File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykatlas/typing/typer/genotyper.py", line 90, in _run_cortex self.mc_cortex_runner.run() File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykatlas/cortex/mccortex.py", line 161, in run self._run_cortex() File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykatlas/cortex/mccortex.py", line 175, in _run_cortex self._run_coverage_if_required() File "/tools/linuxbrew/opt/python3/lib/python3.6/site-packages/mykatlas/cortex/mccortex.py", line 213, in _run_coverage_if_required "mccortex31 raised an error. Is it on PATH? check by running mccortex31 geno. The command that through the error was %s " % subprocess.list2cmdline(self.coverages_cmd)) ValueError: mccortex31 raised an error. Is it on PATH? check by running mccortex31 geno. The command that through the error was /srv/data/AS/RASI/Mykrobe/mccortex/bin/mccortex31 geno -q -t 1 "-m 1GB" -k 15 -o /tmp//test2-15_staph-species-160227-staph-amr-bradley_2015-feb-17-2017.covgs -I /tools/linuxbrew/lib/python3.6/site-packages/mykatlas/atlas/data/skeletons/staph-species-160227-staph-amr-bradley_2015-feb-17-2017_15.ctx -s test2-15 -1 55-100-060_R1.fastq.gz -1 55-100-060_R2.fastq.gz -c /tools/linuxbrew/lib/python3.6/site-packages/mykrobe/data/panels/staph-species-160227.fasta.gz -c /tools/linuxbrew/lib/python3.6/site-packages/mykrobe/data/panels/staph-amr-bradley_2015-feb-17-2017.fasta.gz /tmp//test2-15_staph-species-160227-staph-amr-bradley_2015-feb-17-2017.ctx

[idolawoye]

I have similar issue. Were you able to resolve it? @RaSieb

[iqbal-lab]

Hi all. we are now moving from this repo to a new one, with much updated code: https://github.com/mykrobe-tools/mykrobe could you try this? We will be publicising the new version/repo in a few weeks.

[idolawoye]

Thanks @iqbal-lab the new repo worked perfectly.

[iqbal-lab]

Awesome