Comments (4)
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.
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@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.
from ampliseq.
containers in the context of nf-core pipelines cannot be modified, i.e. nothing can be written in them
from ampliseq.
I see. Thanks for the information.
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Related Issues (20)
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- Add custom qiime reference database support to Ampliseq. HOT 2
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- Error No subject alternative DNS name matching zenodo.org found HOT 2
- minor improvement of sort() before denoising with method = "radix HOT 2
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- Does the `gtdb` database only include Bacteria? HOT 5
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