Error in indexing : do not create SAIndex output file

[PierreL-B]

Hi,
Before August I could create the indexing of a new genome with a GFF file and a FA file when running sequana-rnaseq, but I tried last week and today with sequana version 0.9.5 and sequana_rnaseq 0.9.15 and I have the error in attached file, maybe due to --latency-wait.
What parameter should I change ?
slurm-31821486.txt

Thanks,
Pierre

[cokelaer]

@PierreL-B I have the same pbl indeed. bowtie2 aligner should work at the moment but not the star aligner. I'll look into this issue and we should have a quick fix in a few days

[cokelaer]

@PierreL-B should be fixed by now with new versions on pypi 0.9.6 for sequana and 0.9.20 for sequana_rnaseq. Not sure this fully solve the star issue (indexing should work but mapping may lead to seg fault in some cases; we are looking into this issue)