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Old 12-24-2015, 12:54 AM   #21
Junior Member
Location: china

Join Date: Dec 2015
Posts: 1

hello,all,I think I have solve this problem:
both nohup and ">" would add stdout and stderr to output file,which cause that problem。

"samtools mpileup -ugf F.fna F.sorted.bam -o F.bcf"
instead of
"samtools mpileup -ugf F.fna F.sorted.bam > F.bcf"
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Old 08-11-2017, 01:42 PM   #22
Location: Santa Fe, NM

Join Date: Nov 2013
Posts: 17

Same here, the bcftools that is compiled within samtools is old, and when I compiled a fresh version from github, this error vanished.
Sam Hokin
Computational Scientist, Carnegie and NCGR
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