Type Error : Write()

[idolawoye]

I installed mykrobe on my PC which works and runs fine, but now when I installed it on the server I get this error when I try to run an analysis: sys.stdout.write(nextline) TypeError: write() argument must be str, not bytes Kindly assist me on what to do.

[iqbal-lab]

If you raise an issue about software, you need to tell them enough information that they can understand the problem. What version did you install, what file did you run it on, how exactly did you do it, what exact command line or button presses, what did you see and when.

[idolawoye]

I have this version of mykrobe v0.5.6-0-gbd7923a-dirty installed on the server. I ran it using this command: mykrobe predict ERR552236 tb --seq ERR552236_1.fastq.gz.fastp --threads 16 on one of the TB strains I have. Below is what was shown on-screen:

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
DEBUG:mykatlas.cortex.mccortex:Setting path to mccortex exacutable
DEBUG:mykatlas.cortex.mccortex:Suggested path to mccortex exacutable is invalid: mccortex31
DEBUG:mykatlas.cortex.mccortex:Checking fallback mccortex exacutable file path: /usr/local/bin/mccortex31
DEBUG:mykatlas.cortex.mccortex:Valid path to mccortex exacutable found: /usr/local/bin/mccortex31
DEBUG:mykatlas.cortex.mccortex:Running coverages command:
/usr/local/bin/mccortex31 geno -t 1 -m 1GB -k 21 -o tmp/ERR552236-21_tb-species-170421-tb-walker-probe-set-feb-09-2017.covgs -I atlas/data/skeletons/tb-species-170421-tb-walker-probe-set-feb-09-2017_21.ctx -s ERR552236-21 -1 ERR552236_1.fastq.gz.fastp -c /usr/local/lib/python3.5/dist-packages/mykrobe/data/panels/tb-species-170421.fasta.gz -c /usr/local/lib/python3.5/dist-packages/mykrobe/data/panels/tb-walker-probe-set-feb-09-2017.fasta.gz tmp/ERR552236-21_tb-species-170421-tb-walker-probe-set-feb-09-2017.ctx
Traceback (most recent call last):
  File "/usr/local/bin/mykrobe", line 11, in <module>
    load_entry_point('mykrobe==0.5.6', 'console_scripts', 'mykrobe')()
  File "/usr/local/lib/python3.5/dist-packages/mykrobe/mykrobe_predictor.py", line 125, in main
    args.func(parser, args)
  File "/usr/local/lib/python3.5/dist-packages/mykrobe/mykrobe_predictor.py", line 34, in run_subtool
    run(parser, args)
  File "/usr/local/lib/python3.5/dist-packages/mykrobe/cmds/amr.py", line 134, in run
    cp.run()
  File "/usr/local/lib/python3.5/dist-packages/mykatlas/typing/typer/genotyper.py", line 73, in run
    self._run_cortex()
  File "/usr/local/lib/python3.5/dist-packages/mykatlas/typing/typer/genotyper.py", line 90, in _run_cortex
    self.mc_cortex_runner.run()
  File "/usr/local/lib/python3.5/dist-packages/mykatlas/cortex/mccortex.py", line 179, in run
    self._run_cortex()
  File "/usr/local/lib/python3.5/dist-packages/mykatlas/cortex/mccortex.py", line 196, in _run_cortex
    self._run_coverage_if_required()
  File "/usr/local/lib/python3.5/dist-packages/mykatlas/cortex/mccortex.py", line 254, in _run_coverage_if_required
    self._execute_command(self.coverages_cmd)
  File "/usr/local/lib/python3.5/dist-packages/mykatlas/cortex/mccortex.py", line 232, in _execute_command
    sys.stdout.write(nextline)
TypeError: write() argument must be str, not bytes

[iqbal-lab]

Thanks, will look into it. The input file has .fastp on the end. What kind of file is it?

[idolawoye]

They are fastq files that have been trimmed using fastp. They work fine with mykrobe on my PC