Closed henrikstranneheim closed 3 years ago
@henningonsbring @talnor @sylvinite Could you have a look at this and try to correct these cases? Or let us know if there are code that needs to change in cg or hermes.
Quite a few of there have 0 reads in statusDB. So it seems like it is bad quality data that has not and will not be analysed.
/home/proj/production/microbial/queries/sampleinfo.json and /home/proj/production/microbial/queries/config.log have the wrong path.
In the deliverables file they are called "/home/proj/production/microbial/results/ACC7522_2021.3.10_10.50.46/sampleinfo.json". Does the naming need to updated in microSALT to be ticket_sampleinfo.json or do we update the paths in cg?
The missing file SAMPLE_trimmed_contigs.fasta is currently generated by the uSALT code https://github.com/Clinical-Genomics/microSALT/blob/master/microSALT/utils/job_creator.py#L208 However. Old samples that are being complained about, still need to be updated to "clear" the error status.
I have not seen any crontab fails for this one for a while. Let close and reopen if needed.
My solution to this was to rerun several microsalt cases, but since it seems to be fixed I wont start them.
Description
Cron hiseq.clinical@hasta $CRONIC ${PRODUCTION_HOME}/servers/resources/hasta.scilifelab.se/crontabs/workflow-microsalt-store-completed.sh >> ${LOG_BASE}/cg.workflow-microsalt-store-completed.log 2> >(tee -a ${LOG_BASE}/cg.workflow-microsalt-store-completed.log >&2)
Cronic detected failure for the command: /home/proj/production/servers/resources/hasta.scilifelab.se/crontabs/workflow-microsalt-store-completed.sh
This can be closed when