Hey y'all, I am encountering an issue while using mpileup to construct a consensus sequences from bam alignments. I had left the program to execute over the weekend but it was seemingly stuck on the first input file. No error message just:
[mpileup] 1 samples in 1 input files
This is strange because the bam file is not particularly large only a few mb. The command I executed is:
${z}/samtools-1.2/samtools mpileup -A -u -C50 -m3 -f ${bowtie2_path}.fa ${infile}.bam | ${z}/bin/bcftools view -cg - | vcfutils.pl vcf2fq > ${infile}.fq; {z}/seqtk-master/seqtk seq -A ${infile}.fq > ${infile}.consensus.fas; rm ${infile}.fq
Both samtools and bcftools are versions 1.2. Anyone know what's the cause of this?
[mpileup] 1 samples in 1 input files
This is strange because the bam file is not particularly large only a few mb. The command I executed is:
${z}/samtools-1.2/samtools mpileup -A -u -C50 -m3 -f ${bowtie2_path}.fa ${infile}.bam | ${z}/bin/bcftools view -cg - | vcfutils.pl vcf2fq > ${infile}.fq; {z}/seqtk-master/seqtk seq -A ${infile}.fq > ${infile}.consensus.fas; rm ${infile}.fq
Both samtools and bcftools are versions 1.2. Anyone know what's the cause of this?
