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Old 03-20-2017, 07:57 AM   #1
quantic
Junior Member
 
Location: USA

Join Date: Mar 2017
Posts: 2
Default Issue with mpileup

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?
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