Issues with Humann3 Docker

Microbial community profiling HUMAnN
1

Hello Biobakery Team,

I using the docker version of the latest Humann3 (docker pull biobakery/humann:latest). I am facing an issue with the library GLPK. I had tried using humann3 with conda installation as well, I face a similar issue even after installing the latest GLPK library. Could you please let me how to resolve this? Thanks

GLPSOL: GLPK LP/MIP Solver, v4.55
Parameter(s) specified in the command line:
/humann_temp_wawjnneh/tmphxn44evf/tmp8_vfw1c4
-o humann_temp_wawjnneh/tmphxn44evf/tmp8_vfw1c4.LPout
Reading problem data from ‘/humann_temp_wawjnneh/tmphxn44evf/tmp8_vfw1c4’…
/humann_temp_wawjnneh/tmphxn44evf/tmp8_vfw1c4:1: unexpected end of file
MPS file processing error

Error when running glpsol from MinPath.

Error message returned from glpsol :
GLPSOL: GLPK LP/MIP Solver, v4.55
Parameter(s) specified in the command line:
/humann_temp_wawjnneh/tmphxn44evf/tmpp_oc57rz
-o /humann_temp_wawjnneh/tmphxn44evf/tmpp_oc57rz.LPout
Reading problem data from ‘/humann_temp_wawjnneh/tmphxn44evf/tmpp_oc57rz’…
Problem: PATH
Objective: NUM
/humann_temp_wawjnneh/tmphxn44evf/tmpp_oc57rz:297: warning: missing final end of line
/humann_temp_wawjnneh/tmphxn44evf/tmpp_oc57rz:297: missing row name in field 3
MPS file processing error

CRITICAL ERROR: Unable to process all thread commands.

2

Hello @santoshe1 , Thank you for the detailed post and sorry to hear you are having issues installing GLPK. If you try installing the HUMAnN pypi package from source with the command $ pip install humann --no-binary :all: it will install all of the needed dependencies, including the latest GLPSOL.

Alternatively if you start with a new HUMAnN docker container it should already include the latest packages.

Thank you,
Lauren