How to check whether 'bwa aln' succeeded ?

Question

[deepue]

Hi,

How to check the command "bwa aln" whether completed successfully or not ?

Please provide your views.

Thanks

Answer 1

[Pierre Lindenbaum]

on success, bwa aln returns EXIT_SUCCESS / 0

https://github.com/lh3/bwa/blob/master/bwtaln.c:

...

    }
    bwa_aln_core(prefix, argv[optind+1], opt);
    free(opt); free(prefix);
    return 0;
}

[deepue]

Hi Pierre,

I didn't the message but final message return in the logs I could see are the below:

[bwa_aln_core] calculate SA coordinate... 236.59 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 25949899 sequences have been processed.

Is this value(25949899) of any significance, as it has been written across in another reads alignment as well.

Thanks

[Pierre Lindenbaum]

No, it's just a log on stderr. https://github.com/lh3/bwa/blob/705aa538947a0681de575f0f0d5c65593f80cf14/bwtaln.c#L221 .

See http://bencane.com/2014/09/02/understanding-exit-codes-and-how-to-use-them-in-bash-scripts/

[lh3]

If you are using more recent versions, your alignment is incomplete. Bwa reports the total CPU and real time as the last message.

[deepue]

Hi,

I have used the exit codes in my script

bwa aln -t 4 -f L1_R1_M.sai -I hg19 L1_R1_M.fastq.gz

if [ $? -eq 0 ]
then
  echo "Successfully created .sai file"
else
  echo "Could not create .sai file" >&2
fi

In my output .OU file, I could find the message Successfully created .sai file and even in my error message I found [bwa_aln_core] 25949899 sequences have been processed. as the last line of the file.

So, is it an error or successful completion now?

Note: Available version - bwa (alignment via Burrows-Wheeler transformation) :Version: 0.5.9-r16

Thanks