Entering edit mode
4.7 years ago
CaffeSospeso ▴ 50
I'm usng bwa index command to index the Rattus genome. I used the following command:
bwa index GCF_000001895.5_Rnor_6.0_genomic.fna &> ./error.oe
After indexing I obtain 4 output files .ann, .pac, .bwt, .amb. However, I'm missing output file with .sa format. I cannot then proceed with the following steps of my genomic analyses.
Someone can explain why I do not obtain the .sa file output?
I'm running the bwa index command in a SLURM cluster.
Did the job complete without any errors? Did you allocate enough wall time for it?
Yes, I obtain this info in the log file:
I suppose the log file you showed above is from "error.oe". However, SLURM also saves stderr to a file, did you check this output?
Yes, it is correct. But I did not check the stderr file you are talking about. Or if I did, there were anything.
The index build did not complete, here are the last lines of successful build:
I concur with genomax, your job was probably killed due to time or memory restrictions. SLURM logs should indicate this.
If I have well understood when I run my script in SLURM with sbatch, it should give me a log file such as slurm-999696.out ...correct? Now I'm re-running the bwa index command. In case it is a problem due to time or memory restrictions, what I should do?
Increase time or memory reservations.
It worked by increasing memory. Thank you.