Hi everyone,
I ran some alignments using the bwa - samtools pipeline and now I am in the process of calling the consensus sequence. Everything has worked fine so far, but I have just hit a brick wall. After running the pileup command, the samtools works for a while and then crashes giving me the following error:
samtools: bam_pileup.c:112: resolve_cigar2: Assertion `s->k < c->n_cigar' failed
I searched through the forums and could only find one thread about this, where a person used CG to convert their files into BAM format, which generated the above error. In my case I have used the "samtools view" command to convert my files from SAM to BAM so I don't think this could be the issue.
If anyone has any suggestions I would greatly appreciate it.
By the way, the command I've been using is:
samtools pileup -vcf [input.fasta] [input.aln.sorted.bam] > [output.txt]
Thanks!
PS. I've been wondering (and trying to figure out) if my starting fastq files are the issue. They are in Illumina 1.5 format, and I never specified that my files are Illumina-format in the pipeline (supposedly bwa mem works for this).
I ran some alignments using the bwa - samtools pipeline and now I am in the process of calling the consensus sequence. Everything has worked fine so far, but I have just hit a brick wall. After running the pileup command, the samtools works for a while and then crashes giving me the following error:
samtools: bam_pileup.c:112: resolve_cigar2: Assertion `s->k < c->n_cigar' failed
I searched through the forums and could only find one thread about this, where a person used CG to convert their files into BAM format, which generated the above error. In my case I have used the "samtools view" command to convert my files from SAM to BAM so I don't think this could be the issue.
If anyone has any suggestions I would greatly appreciate it.
By the way, the command I've been using is:
samtools pileup -vcf [input.fasta] [input.aln.sorted.bam] > [output.txt]
Thanks!
PS. I've been wondering (and trying to figure out) if my starting fastq files are the issue. They are in Illumina 1.5 format, and I never specified that my files are Illumina-format in the pipeline (supposedly bwa mem works for this).
Comment