parse error with samtools

Question

[a.rex]

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?

[WouterDeCoster]

I don't think there is a good reason to use sudo in this command. If you don't absolutely have to, don't.

[Ram]

Sometimes I'm glad Apple implemented SIP. Rogue sudos can wreak havoc.

[a.rex]

Thanks - sudo is not needed, silly mistake

[WouterDeCoster]

I can't decipher what's wrong with your parallel command... Tagging ole.tange

You can use parallel --dryrun to see how the command is going to be ran, i.e. print the command string. And then check if that's as expected.