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Hi all
This is my first post here although I have been reading discussions for a while and it has helped me no end. I am trying to pass a named pipe to the samtool mpileup command but it complains of a broken pipe.
I get the data being piped in as expected after the 'tee' command and the testmpilup.txt file is populated but when I pass the named pipe ie 'input.fifo' to the mpileup command, I get a Broken pipe error message and the Variants.vcf file is not populated. I know I can pass the command twice for samtools view and I probably won't lose that much processing time but I successfully implemented this approach on another part of my pipeline but wondered why I can't do the same here.
Any ideas?
This is my first post here although I have been reading discussions for a while and it has helped me no end. I am trying to pass a named pipe to the samtool mpileup command but it complains of a broken pipe.
Code:
mkfifo input.fifo /samtools mpileup -EDSgu -d 5000 -f /Homo_sapiens.GRCh37.73.dna.primary_assembly.fa -L 5000 -F 0.05 input.fifo -> /Variants.vcf & /samtools view -bq 20 -F 1796 /bamfile.bam | tee input.fifo | /samtools mpileup -EDS -d 5000 -f /Homo_sapiens.GRCh37.73.dna.primary_assembly.fa -L 5000 -F 0.05 -> /testmpileup.txt The Output shows the following error Running tool: Run command tee: input.fifo: Broken pipe [bam_header_read] EOF marker is absent. The input is probably truncated. [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000
I get the data being piped in as expected after the 'tee' command and the testmpilup.txt file is populated but when I pass the named pipe ie 'input.fifo' to the mpileup command, I get a Broken pipe error message and the Variants.vcf file is not populated. I know I can pass the command twice for samtools view and I probably won't lose that much processing time but I successfully implemented this approach on another part of my pipeline but wondered why I can't do the same here.
Any ideas?