bwa index with no .sa file
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5.8 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 • 3.9k views
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Did the job complete without any errors? Did you allocate enough wall time for it?

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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...
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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?

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

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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.

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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?

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Increase time or memory reservations.

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It worked by increasing memory. Thank you.

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