nickp60/ezclermont

Phylotype your strains using Clermont's 2013 method: ezclermont.org

ezclermont's Issues

Pip install failed

Hello Nick,

I tried installing EzClermont, following step by step. It was going well...

conda create -n ezclermont biopython
conda activate ezclermont

• I think it should be conda create -n ezclermont biopython, not conda create -n ez biopython

... until it failed at the pip install stage

(ezclermont) ahbui@TUF[~] pip install ezclermont
Collecting ezclermont
  Downloading ezclermont-0.6.2.tar.gz (13 kB)
    ERROR: Command errored out with exit status 1:
     command: /home/ahbui/Zarul/Software/anaconda3/envs/ezclermont/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-0qpruu7b/ezclermont_ca821db144f847fc8d845181fc60f073/setup.py'"'"'; __file__='"'"'/tmp/pip-install-0qpruu7b/ezclermont_ca821db144f847fc8d845181fc60f073/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-q6cvphlz
         cwd: /tmp/pip-install-0qpruu7b/ezclermont_ca821db144f847fc8d845181fc60f073/
    Complete output (7 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-0qpruu7b/ezclermont_ca821db144f847fc8d845181fc60f073/setup.py", line 38, in <module>
        requirements = [str(ir.req) for ir in install_reqs]
      File "/tmp/pip-install-0qpruu7b/ezclermont_ca821db144f847fc8d845181fc60f073/setup.py", line 38, in <listcomp>
        requirements = [str(ir.req) for ir in install_reqs]
    AttributeError: 'ParsedRequirement' object has no attribute 'req'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Can you try and see what happened please?

Thank you.

Different result with ClermonTyping

Hello again @nickp60,

I caught an inconsistency between EzClermont (CLI) and ClermonTyping (webapp: http://clermontyping.iame-research.center/index.php).

[arpA, chuA, yjaA, TspE4.C2]
EzClermont: [- - + -] cryptic
ClermonTyping: [+ - + -] A

I am trying to figure out why is this happening.
Attached the genome in question.
3817_AV78.zip

Thanks!

Output to stderr

Hi Nick,

Nice work with this software, the conda package and Docker images work a treat stand-alone.

However, I'm currently trying to integrate EzClermont into a Nextflow analysis pipeline and it seems to me that the fact the PCR output is sent to stderr causes the pipeline to fail as Nextflow fairly assumes any output by a program to stderr denotes a genuine error and stops the pipeline. So I was wondering if it would be possible to define output files instead of streaming to stdout/stderr or alternatively if the stderr output could be silenced?

Cheers,

Cam

Phylogroup G prediction

Hi! I was wondering if EzClermont can predict phylogroup G as per https://doi.org/10.1111/1462-2920.14713

Thanks!

Result not present in docs

We ran a pile of contigs for an environmental E. coli strain through the web server. It returned "U", which I'm guessing means "unknown"? This outcome is not referenced in the publication or docs.