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Hi,
I observed a strange thing. I am running bwa for around 7 million reads of size 36 using the command "bwa aln -n 5 -f out.map db_prefix input.fastq"
and while it was still running I made a copy of out.map and converted it to sam format (using samse option) to give out.sam file. When I checked the out.sam file, it already has mapping data for ALL 7 million reads but the bwa aln is still running and the out.map's size is increasing and the statement "calculate SA coordinate..." is being printed to the console intermittently. I do not understand as to what is bwa still writing to the out.map file when the mapping coordinates for all reads is already calculated. I am quite new to bwa (have used MAQ before) and thus need your help to understand it.
Thanks for the support,
Ramya
I observed a strange thing. I am running bwa for around 7 million reads of size 36 using the command "bwa aln -n 5 -f out.map db_prefix input.fastq"
and while it was still running I made a copy of out.map and converted it to sam format (using samse option) to give out.sam file. When I checked the out.sam file, it already has mapping data for ALL 7 million reads but the bwa aln is still running and the out.map's size is increasing and the statement "calculate SA coordinate..." is being printed to the console intermittently. I do not understand as to what is bwa still writing to the out.map file when the mapping coordinates for all reads is already calculated. I am quite new to bwa (have used MAQ before) and thus need your help to understand it.
Thanks for the support,
Ramya