BLR appears to still be running despite generation of MultiQC report

[ajdesalvio]

Hi Pontus,

I hope you're doing well! I've resumed using BLR to analyze a few more samples recently. One of them appears to have completed, but the SLURM job I submitted is still active after 48 hours of inactivity and I was wondering if you've encountered this before. The final MultiQC report was generated (link to the file here) and the last few lines of the .err file indicate that the final.barcodes.bam file was produced along with its index (final.barcodes.bam.bai) (attached and also available via the link). Would you mind looking to see if it's safe to terminate the job? I would just hate to waste kilowatts if something is actually not finished. As always, I am grateful for your time and for making this pipeline!

Sincerely,

Aaron

tellseq_ktz2.err.txt

[pontushojer]

Hi Aaron, I guess they might have finished by now if they have been running over the weekend :)

If not, it depends on what you are interested in. From your log it seems that the at least the manta process is still running, not sure if there are others. If it is only the manta process and you do not care about manta SV calls or by extension large insertions (via MTG-link that rely on manta output) you are free to stop the process.

[ajdesalvio]

Hi Pontus,

That is indeed the case, so I will likely stop the process! I think the phased BAM and VCF are our primary aims. The output files in the manta folder haven't been updated in several days also, so I am not sure if it finished or ever initialized. The log only contains these lines:

Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

/scratch/user/aarondesalvio/Serina/TellSeq2/Outputs_V3/KTZ_2_V4/Outputs/manta_tmp/runWorkflow.py

Thanks again!