A BWA running problem for

[davidwang]

I am using the BWA (Version: 0.7.5a-r405) to analyze exome sequencing data. When I ran the 4) programming, error happened as shown below 4).

1) bwa index -a bwtsw hg19.fa
2) bwa aln -t 4 hg19.fa 1W44RAP_CGATGT_L001_R1_001.fastq > 1W44RAP_CGATGT_L001_R1_001.fastq.sai
3) bwa aln -t 4 hg19.fa 1W44RAP_CGATGT_L001_R2_001.fastq > 1W44RAP_CGATGT_L001_R2_001.fastq.sai
4) bwa sampe hg19.fa 1W44RAP_CGATGT_L001_R1_001.fastq.sai 1W44RAP_CGATGT_L001_R2_001.fastq.sai 1W44RAP_CGATGT_L001_R1_001.fastq 1W44RAP_CGATGT_L001_R2_001 > 1W44_001.sam

[E::bwa_sai2sam_pe_core] Unmatched SAI magic. Please re-run `aln' with the same version of bwa.

I don't know what's the problem and how to resolve it.
Thanks.

Davd Wang

[vivek_]

4) bwa sampe hg19.fa 1W44RAP_CGATGT_L001_R1_001.fastq.sai 1W44RAP_CGATGT_L001_R2_001.fastq.sai 1W44RAP_CGATGT_L001_R1_001.fastq 1W44RAP_CGATGT_L001_R2_001 > 1W44_001.sam

Are you sure its not because of missing the .fastq extension on the command line here?

[davidwang]

no. I had the .fastq extension

Are you sure its not because of missing the .fastq extension on the command line here?

I had the .fastq extension