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Old 08-09-2011, 09:11 AM   #1
Location: Utah

Join Date: Dec 2010
Posts: 14
Default running samtools mpileup with nohup -redirect STDERR?

I have seen multiple people getting this error - when piping mpileup into bcftoos -
[bcf_sync] incorrect number of fields (0 != 5). Corrupted file?
I was getting this error until I saw this command does not work without redirecting STDERR -
can someone tell me how to do this so I can run this command with nohup?

samtools mpileup -I -C 0 -Q 40 -u -f /hg19.fasta /7623X1_Converted_reheaded.bam | bcftools view -vcg - > /7623X1.var.raw3
12jrowley2 is offline   Reply With Quote
Old 08-09-2011, 10:24 AM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

The bcftools view command is loads faster than the mpileup, you could run the sequentially. You won't lose much time.
swbarnes2 is offline   Reply With Quote

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