How to check whether 'bwa aln' succeeded ?
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6.7 years ago
deepue ▴ 150

Hi,

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

Please provide your views.

Thanks

sequencing alignment • 2.1k views
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6.7 years ago

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;
}
 
 
 
 
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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

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

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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

 

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