Problems with miRTrace output

[lcabus-flomics]

Hi, I was running the pipeline with 40 samples and everything worked well, but at the end I didn't obtain the mirtrace files (mirtrace-report.html, mirtrace-results.json, etc.), I only obtained the qc_passed_reads.all.collapsed and qc_passed_reads.rnatype_unknown.collapsed. Nonetheless, the pipeline was completed successfully and I think that there are no other errors. When I run the pipeline only with 10 samples everything seems to work well, I don't know which can be the problem...

Thank you very much!

[shashwatsahay]

This used to happen with me, were you running on a cluster if yes then you should in the cluster config file, assign more memory to processes

[lcabus-flomics]

Hi, I tried assigning more memory in general and specifically in the miRTrace process, but it still failed. I finally installed miRTrace and run it that way, but still the problem is still there. How many memory did you use? I have a put as a maximum amount of resources 200GB and 16 cpus.

[shashwatsahay]

Can you share the log files? it would be something like .nextflow.log

Also in the .nextflow.log get the logs from mirTrace work dir (the temp folder that is created) also

[lcabus-flomics]

Hi, sorry, I was doing some tests and I had to rerun the pipeline.

nextflow.log

in the .command.log in the miRTrace work dir I have: miRTrace version 1.0.0 starting. Processing 40 sample(s).

The .command.err contains exactly the same: miRTrace version 1.0.0 starting. Processing 40 sample(s).

[apeltzer]

This should nowadays not be an issue at all anymore - please give things a try (if you can / still want to) using -r dev.