Error when running command MinPath12hmp.py

Microbial community profiling HUMAnN
1

Dear developers,

I have problem when using humann2 v2.8.1 .

Here is the error information from log file:

03/19/2020 06:31:25 PM - humann2.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
File “/home/bayegy/pipelines/metagenome/miniconda2/lib/python2.7/site-packages/humann2/utilities.py”, line 733, in execute_command
p = subprocess.check_call(cmd, stdin=stdin, stdout=stdout, stderr=stderr)
File “/home/bayegy/pipelines/metagenome/miniconda2/lib/python2.7/subprocess.py”, line 190, in check_call
raise CalledProcessError(retcode, cmd)
CalledProcessError: Command ‘[’/home/bayegy/pipelines/metagenome/miniconda2/bin/python’, ‘/home/bayegy/pipelines/metagenome/miniconda2/lib/python2.7/site-packages/humann2/quantify/MinPath12hmp.py’, ‘-any’, ‘/media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpfDJyhA’, ‘-map’, ‘/media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpEgTm3s’, ‘-report’, ‘/media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpt9eV_P’, ‘-details’, ‘/media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpyJ4oRY’, ‘-mps’, ‘/media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpnCx5DD’]’ returned non-zero exit status 1

03/19/2020 06:31:25 PM - humann2.utilities - INFO: Execute command: /home/bayegy/pipelines/metagenome/miniconda2/bin/python /home/bayegy/pipelines/metagenome/miniconda2/lib/python2.7/site-packages/humann2/quantify/MinPath12hmp.py -any /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpN0GicT -map /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpEgTm3s -report /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmp9cnoNV -details /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpFwC18S -mps /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpiIV39U
03/19/2020 06:31:28 PM - humann2.utilities - CRITICAL:
CRITICAL ERROR: Unable to process all thread commands.

Error message returned from command for thread task 25: /home/bayegy/pipelines/metagenome/miniconda2/bin/python /home/bayegy/pipelines/metagenome/miniconda2/lib/python2.7/site-packages/humann2/quantify/MinPath12hmp.py -any /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpfDJyhA -map /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpEgTm3s -report /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpt9eV_P -details /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpyJ4oRY -mps /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpnCx5DD

So I ran the command referred in error information, and I got this:

now write mps file…
original ortholog=4 found-in-the-fam-list=0 found-in-the-fam-mapped-to-pathway=0
End of PrintMPS
Error when running glpsol from MinPath.

Error message returned from glpsol :
load_mps: reading LP data from /media/bayegy/disk2/Projects/zhangyaqin/result/Metagenome/Humann/HUA34/HUA34_humann2_temp/tmpan1iKT/tmpnCx5DD'... load_mps: name PATH’
load_mps: 1 rows
load_mps: 0 columns
load_mps: 0 non-zeros
load_mps: 0 right-hand side vector(s)
load_mps: 0 range vector(s)
load_mps: 0 bound vector(s)
load_mps: 7 cards were read
lpx_add_cols: ncs = 0; invalid number of columns

Any clues to help me out? Thanks!

2

Sorry for the delay. It looks like you might need to upgrade glpk to solve this issue. There is a thread about this in the archived HUMAnN Google Group that might be of use to you:

https://groups.google.com/d/topic/humann-users/MSVmXC7DSW0/discussion

3

I had the same issue. I managed to fix it by explicitly installing the glpk package via conda. The humann2 meta.yaml file should probably be updated in the bioconda-recipe.

Cheers,
John

4

I believe the bioconda HUMAnN recipe was submitted by someone else, so it’s harder for us to stay on top of the errors there. If you install from the biobakery conda channel you’ll know it’s a recipe we put together and tested.

5

Good to know! Thanks!

6

@johnne
@franzosa
Thanks, best wishes