I have some MiSeq data that I am trying to align with BWA to hg19.
This is the command:
bwa sampe -P <dir>/BWAIndex/genome.fa 1_1.sai 1_2.sai 1_1.fastq 1_2.fastq > out.sam
This is the output I am seeing:
It outputs a BAM file, but nothing is aligned. The same data was processed through Illumina's BaseSpace service, which uses BWA, and it produced results, so there should not be anything wrong with the actual reads. I also tried aligning with Bowtie2 and got reasonable results, so the FASTQ files should not be corrupted.
I have no idea what's wrong and I can't seem to find any record of such an error anywhere online. How do I troubleshoot this?
This is the command:
bwa sampe -P <dir>/BWAIndex/genome.fa 1_1.sai 1_2.sai 1_1.fastq 1_2.fastq > out.sam
This is the output I am seeing:
Code:
[bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] fail to infer insert size: too few good pairs [bwa_sai2sam_pe_core] time elapses: 0.10 sec [bwa_sai2sam_pe_core] changing coordinates of 0 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_sai2sam_pe_core] time elapses: 0.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.10 sec [bwa_sai2sam_pe_core] print alignments... 1.06 sec [bwa_sai2sam_pe_core] 262144 sequences have been processed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] fail to infer insert size: too few good pairs [bwa_sai2sam_pe_core] time elapses: 0.06 sec [bwa_sai2sam_pe_core] changing coordinates of 0 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_sai2sam_pe_core] time elapses: 0.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.08 sec [bwa_sai2sam_pe_core] print alignments... 1.13 sec [bwa_sai2sam_pe_core] 524288 sequences have been processed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] fail to infer insert size: too few good pairs [bwa_sai2sam_pe_core] time elapses: 0.01 sec [bwa_sai2sam_pe_core] changing coordinates of 0 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_sai2sam_pe_core] time elapses: 0.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.01 sec [bwa_sai2sam_pe_core] print alignments... 0.16 sec [bwa_sai2sam_pe_core] 569473 sequences have been processed. [main] Version: 0.6.2-r126
I have no idea what's wrong and I can't seem to find any record of such an error anywhere online. How do I troubleshoot this?
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