Hi All,
I have ~100M Illumina RNA-Seq file in fastq format. After I ran BWA algn against trascriptome(all available cDNAs in fasta format, indexed by BWA), I got ~300M sai file. Then I ran BWA samse to generate sam file. However, BWA samse did not output anymore sam record when its size is ~5M. I've checked sam file and found BWA stopped at some SQ header output. None alignment is reported and it has ran for over 50 hours so far. There must be something wrong. Does anybody face the same issue?
I have ~100M Illumina RNA-Seq file in fastq format. After I ran BWA algn against trascriptome(all available cDNAs in fasta format, indexed by BWA), I got ~300M sai file. Then I ran BWA samse to generate sam file. However, BWA samse did not output anymore sam record when its size is ~5M. I've checked sam file and found BWA stopped at some SQ header output. None alignment is reported and it has ran for over 50 hours so far. There must be something wrong. Does anybody face the same issue?