Dear users,
I have run bwa on microRNA reads from ABI solid and I generated a file aln.sam.
But when I try to import this file in samtools, the program returns me different errors.
I can't convert SAM to BAM.
I'm using samtools-0.1.7
if I run:
>samtools import reference.fasta.fai aln.sam prova.bam
the error is
[sam_header_read2] 735 sequences loaded.
Parse error at line 1: invalid CIGAR character
Aborted
If I run:
>samtools import reference.fasta aln.sam prova.bam
the error
[sam_header_read2] 1102 sequences loaded.
Segmentation fault
With:
>samtools view aln.sam prova.bam
[bam_header_read] EOF marker is absent.
[main_samview] fail to read the header.
>samtools view -S aln.sam -o prova.bam
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
>samtools view -S aln.sam prova.bam
[samopen] no @SQ lines in the header.
[main_samview] random alignment retrieval only works for indexed BAM files.
I can only think that the problem is the header of sam file.
But what can I do?
Thanx!
I have run bwa on microRNA reads from ABI solid and I generated a file aln.sam.
But when I try to import this file in samtools, the program returns me different errors.
I can't convert SAM to BAM.
I'm using samtools-0.1.7
if I run:
>samtools import reference.fasta.fai aln.sam prova.bam
the error is
[sam_header_read2] 735 sequences loaded.
Parse error at line 1: invalid CIGAR character
Aborted
If I run:
>samtools import reference.fasta aln.sam prova.bam
the error
[sam_header_read2] 1102 sequences loaded.
Segmentation fault
With:
>samtools view aln.sam prova.bam
[bam_header_read] EOF marker is absent.
[main_samview] fail to read the header.
>samtools view -S aln.sam -o prova.bam
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
>samtools view -S aln.sam prova.bam
[samopen] no @SQ lines in the header.
[main_samview] random alignment retrieval only works for indexed BAM files.
I can only think that the problem is the header of sam file.
But what can I do?
Thanx!
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