I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. I am able to successfully generate an index (using the hisat2-build command), but when it comes to the actual mapping, I run into problems. The code I'm using (from the paper):

$hisat2 -p 8 --dta -x daphnia_tran -1 C2*R1*.fastq -2 C2*R2*.fastq -S C2paired.sam

And I get the error message:

./HISAT2_Basic_14.sh: line 26: -p: command not found

When I remove the -p argument, the error message is similar, but says "--dta: command not found"

Any ideas on what the issue is?

Thank you!


tldr: Remove the $ from the command.

I imagine you're literally typing $hisat2, where you mean to instead type hisat2. The $ is just meant to show the end of the command prompt. If you actually type $hisat2, you're not executing the hisat2 program, but whatever the $hisat2 variable is set to. Since it's likely not set to anything, it's just ignored. For example:

ryan@maximus:~$ $hisat2 ls
bin              convertChromosomesChain.py  ...

Since there's no $hisat2 variable, I'm actually just running ls. Likewise, your command is just reducing to -p 8 --dta -x daphnia_tran -1 C2*R1*.fastq -2 C2*R2*.fastq -S C2paired.sam, which is the source of the error.

  • $\begingroup$ Can't believe I missed that, thanks very much! The script seems to be running perfectly now. $\endgroup$
    – genome454
    Mar 13 '18 at 16:05

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