flye crash in population_assembly step

shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

MIT License

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flye crash in population_assembly step #78

Open alanorth opened 2 years ago

alanorth commented 2 years ago

While running the test data with hecatomb 1.0.0 (manually patched for #76 and #77), flye crashes with a Python error. From hecatomb_out/STDERR/population_assembly.flye.log:

Could not find platform independent libraries <prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Fatal Python error: initfsencoding: Unable to get the locale encoding
LookupError: no codec search functions registered: can't find encoding

Current thread 0x00002b71f79c7ec0 (most recent call first):

beardymcjohnface commented 2 years ago

Hi Alan, Sorry for the late reply, I just got back from leave. Have you had any success troubleshooting this issue? If this is the only error you are getting then I would guess that something has gone wrong with conda env. There are a few google hits for this error, nothing specific to flye but looks like it crops up with corrupted virtual environments etc. I would try manually installing flye into a new env and checking if it runs.

alanorth commented 2 years ago

Thank you, @shandley. The user is re-running the job and it hasn't gotten to the flye step yet. Will keep you posted. We have to keep fixing the envs every so often (based on our other issues #76 #77).