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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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mykrobe predictor error #125

Closed vsrinivasanoucru closed 5 years ago

vsrinivasanoucru commented 7 years ago

I installed mykrobe and when I try to do AMR predict, I am facing some problem.

ubuntu@vsrinivasan:~/mtb_genome$ mykrobe predict SRR648517 tb -1 SRR648517.fastq.gz INFO:root:Running AMR prediction with panels data/panels/tb-species-160330.fasta.gz, data/panels/tb-walker-probe-set-feb-09-2017.fasta.gz [18 May 2017 09:37:12-zEM][file_util.c:169] Fatal Error: Cannot write to file: /usr/local/lib/python3.4/dist-packages/mykatlas/atlas/data/skeletons/tb-species-160330-tb-walker-probe-set-feb-09-2017_21.ctx [Permission denied] Traceback (most recent call last): File "/usr/local/bin/mykrobe", line 11, in load_entry_point('mykrobe==0.5.1', 'console_scripts', 'mykrobe')() File "/usr/local/lib/python3.4/dist-packages/mykrobe/mykrobe_predictor.py", line 125, in main args.func(parser, args) File "/usr/local/lib/python3.4/dist-packages/mykrobe/mykrobe_predictor.py", line 34, in run_subtool run(parser, args) File "/usr/local/lib/python3.4/dist-packages/mykrobe/cmds/amr.py", line 134, in run cp.run() File "/usr/local/lib/python3.4/dist-packages/mykatlas/typing/typer/genotyper.py", line 73, in run self._run_cortex() File "/usr/local/lib/python3.4/dist-packages/mykatlas/typing/typer/genotyper.py", line 90, in _run_cortex self.mc_cortex_runner.run() File "/usr/local/lib/python3.4/dist-packages/mykatlas/cortex/mccortex.py", line 161, in run self._run_cortex() File "/usr/local/lib/python3.4/dist-packages/mykatlas/cortex/mccortex.py", line 173, in _run_cortex self._build_panel_binary_if_required() File "/usr/local/lib/python3.4/dist-packages/mykatlas/cortex/mccortex.py", line 191, in _build_panel_binary_if_required subprocess.check_output(cmd) File "/usr/lib/python3.4/subprocess.py", line 620, in check_output raise CalledProcessError(retcode, process.args, output=output) subprocess.CalledProcessError: Command '['mccortex31', 'build', '-q', '-m 1GB', '-t', '1', '-k', '21', '-s', 'tb-species-160330-tb-walker-probe-set-feb-09-2017', '-1', '/usr/local/lib/python3.4/dist-packages/mykrobe/data/panels/tb-species-160330.fasta.gz', '-1', '/usr/local/lib/python3.4/dist-packages/mykrobe/data/panels/tb-walker-probe-set-feb-09-2017.fasta.gz', '/usr/local/lib/python3.4/dist-packages/mykatlas/atlas/data/skeletons/tb-species-160330-tb-walker-probe-set-feb-09-2017_21.ctx']' returned non-zero exit status 1

Kindly let me know where is the problem.

iqbal-lab commented 6 years ago

I've just realised this issue has been open and ignored! Apologies to vsrinivasanoucru We will look into this . This seems significant:

Fatal Error: Cannot write to file: /usr/local/lib/python3.4/dist-packages/mykatlas/atlas/data/skeletons/tb-species-160330-tb-walker-probe-set-feb-09-2017_21.ctx [Permission denied]

Have you installed it somewhere where it/you dont have write access?

vsrinivasanoucru commented 6 years ago

Hi I have solved the problem with the help of Phel

"It looks like you installed mykrobe using sudo so you'll also need to run it with sudoe.

e.g. sudo mykrobe predict SRR648517 tb -1 SRR648517.fastq.gz".

Thanks and regards