Debug information for docker-based run.

[hh1985]

Hi,

I am curious about checking the debug information of the modules. I use docker instead of local applications for the pipeline, and received error like:

IIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Plugin error from diversity:

  Command '['run_adonis.R', '/tmp/tmpjv373klr/dm.tsv', '/tmp/tmpjv373klr/md.tsv', 'Class*Gender', '999', '2', '/tmp/qiime2-temp-y3jomxzy/adonis.tsv']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-r8gqpl5p.log

However, the path /tmp/qiime2-q2cli-err-r8gqpl5p.log was unavailable probably because the use of docker container.

[d4straub]

Hi there,
the information you gave is a little scarce, but I assume you run the pipeline on a HPC. In that case, /tmp/ might be on the compute node the job was sent to (if you use a scheduler such as slurm), instead of on the headnode (where you started nextflow), which you might have checked.
This might be a general question about /tmp/ location/accessibility rather than a ampliseq specific question.

[hh1985]

@d4straub I run the pipeline with -profile docker on a ubuntu workstation with 32 threads and 256 GB memory. There're no other nodes. I assume the /tmp/**.log should be on my system but couldn't find them.

As a comparion, I also installed the qiime2 separately and ran the same command successfully. This time I can access the /tmp/**.log file and quickly identified the error. I guess the issue with ampliseq pipeline might be the use of docker container, where the /tmp/**.log file was not moved to a shared drive.

[d4straub]

containers in the context of nf-core pipelines cannot be modified, i.e. nothing can be written in them

[hh1985]

I see. Thanks for the information.