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biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
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Humann Failed! Error message : Error executing action 0. Original Exception: #21

Closed imonteroo closed 2 years ago

imonteroo commented 2 years ago

Hi:

I am havinf problems with this workflow. It could run kneaddata and petaphlan (with --bypass-functional-profiling --bypass-strain-profiling options), but, when I try to run humann or strainphlan, I receive task failed errors always.

My last code was this:

biobakery_workflows wmgx --input /media/microviable/d/DATOSSECUENCIACION/MVT-prj10_rendimiento_deportivo/BIKE/ --output /media/microviable/e/workflows_output --local-jobs 2 --threads 4 --bypass-strain-profiling

And this is the file: anadama.log

I would appreciate any help.

This is the part

2022-02-02 22:35:28,286 LoggerReporter log_event INFO: task 135, humann____BIKE011B_lib527520_7698_3 : starting to run 2022-02-02 22:35:28,415 LoggerReporter task_command INFO: Tracked executable version: humann v3.0.0.alpha.4

2022-02-02 22:35:28,415 LoggerReporter task_command INFO: Executing with shell: humann --input /media/microviable/e/workflows_output/kneaddata/main/BIKE011B_lib527520_7698_3.fastq --output /media/microviable/e/workflows_output/humann/main --o-log /media/microviable/e/workflows_output/humann/main/BIKE011B_lib527520_7698_3.log --threads 4 --taxonomic-profile /media/microviable/e/workflows_output/metaphlan/main/BIKE011B_lib527520_7698_3_taxonomic_profile.tsv
2022-02-02 22:35:28,416 LoggerReporter log_event INFO: task 136, humann____BIKE011C_lib527528_7698_2 : starting to run 2022-02-02 22:35:28,536 LoggerReporter task_command INFO: Tracked executable version: humann v3.0.0.alpha.4

2022-02-02 22:35:28,548 LoggerReporter task_command INFO: Executing with shell: humann --input /media/microviable/e/workflows_output/kneaddata/main/BIKE011C_lib527528_7698_2.fastq --output /media/microviable/e/workflows_output/humann/main --o-log /media/microviable/e/workflows_output/humann/main/BIKE011C_lib527528_7698_2.log --threads 4 --taxonomic-profile /media/microviable/e/workflows_output/metaphlan/main/BIKE011C_lib527528_7698_2_taxonomic_profile.tsv
2022-02-03 00:21:34,856 LoggerReporter log_event INFO: task 137, humannBIKE011D_lib527536_7690_4 : starting to run 2022-02-03 00:21:34,855 LoggerReporter task_failed ERROR: task 135, humannBIKE011B_lib527520_7698_3 : Failed! Error message : Error executing action 0. Original Exception: Traceback (most recent call last): File "/home/microviable/.local/lib/python3.8/site-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/home/microviable/.local/lib/python3.8/site-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/home/microviable/.local/lib/python3.8/site-packages/anadama2/util/init.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 137] Command `humann --input /media/microviable/e/workflows_output/kneaddata/main/BIKE011B_lib527520_7698_3.fastq --output /media/microviable/e/workflows_output/humann/main --o-log /media/microviable/e/workflows_output/humann/main/BIKE011B_lib527520_7698_3.log --threads 4 --taxonomic-profile /media/microviable/e/workflows_output/metaphlan/main/BIKE011B_lib527520_7698_3_taxonomic_profile.tsv ' failed. Out: b'' Err: b'Killed\n'

github-actions[bot] commented 2 years ago

Thank you for creating this issue. We currently field issues through our bioBakery Discourse Support Forum. If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.