When I use new version BWA 0.7.5a to align my 78bp pair-end reads with reference genome under Linux, Index the genome and generate alignments in thesuffix array coordinate, everything went well... However, when I apply generating alignments in the SAM format, it showed unexpected end of file. Then I upload my pair-end reads to Galaxy platform and apply the BWA for Illumina alignment tool. it showed
The alignment failed. Error generating alignments. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] fail to infer insert size: too few good pairs
I used the commands in Linux as follows and believe Galaxy should use the same too...
Bwa index -a bwtsw ref.fa
Bwa aln ref.fa read.fq.gz > Read.sai
Bwa sampe ref.fa read.sai read.fa.gz > aln.sam
I do not figure out what is the problem is? My forward reads are very good after QC ( no duplicates, no overrepresent sequence and no Kmer sequence) and my reverse reads are ok ( no dupdlicates, no overrepresent sequence but has some Kmer sequences).
Is that possible that my reverse reads are bad for BWA alignment and following steps???