bwa index with no .sa file
0
1
Entering edit mode
6.1 years ago
CaffeSospeso ▴ 50

Hello,

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.

genome • 4.0k views
ADD COMMENT
0
Entering edit mode

Did the job complete without any errors? Did you allocate enough wall time for it?

ADD REPLY
0
Entering edit mode

Yes, I obtain this info in the log file:

bwa_index] Pack FASTA... 43.06 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5740368386, availableWord=415913560
[BWTIncConstructFromPacked] 10 iterations done. 99999986 characters processed.
..... (points are to not include the entire log file)
BWTIncConstructFromPacked] 640 iterations done. 5737287298 characters processed.
[bwa_index] 4382.12 seconds elapse.
[bwa_index] Update BWT...
ADD REPLY
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

Yes, it is correct. But I did not check the stderr file you are talking about. Or if I did, there were anything.

ADD REPLY
1
Entering edit mode

The index build did not complete, here are the last lines of successful build:

[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa index contigs_2.fasta
[main] Real time: 0.018 sec; CPU: 0.008 sec

I concur with genomax, your job was probably killed due to time or memory restrictions. SLURM logs should indicate this.

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

Increase time or memory reservations.

ADD REPLY
0
Entering edit mode

It worked by increasing memory. Thank you.

ADD REPLY

Login before adding your answer.

Traffic: 899 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6