parse error with samtools
I am using the following parallel command to run hisat on individual files, and pipe the output to make a new bam file:
sudo parallel echo “./hisat2 --dta -p 32 -x /pathtoindex/index -U {} \| ./samtools view -b - \> /path/to/output/{/.}.bam” :::: fs > bam.sh
fs contains a list of my file paths, and bam.sh is my executable.
However, when I run this I get the following error:
[W::sam_read1] parse error at line 1
[main_samview] truncated file.
Is there something wrong with my parallel command that samtools does not seem to like?
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I don't think there is a good reason to use sudo in this command. If you don't absolutely have to, don't.
Sometimes I'm glad Apple implemented SIP. Rogue
sudos can wreak havoc.Thanks - sudo is not needed, silly mistake
I can't decipher what's wrong with your parallel command... Tagging ole.tange
You can use
parallel --dryrunto see how the command is going to be ran, i.e. print the command string. And then check if that's as expected.