juicer.sh SLURM script

[aidenlab]

juicer.sh SLURM script

[imachol]

Oh, this is bash version dependent issue.
Were checking if variable is defined, not empty.

If it does not work for you, try
[ -z ${shortread+x} ]
Instead.

[keagen]

Ok. That fixed the error message.

Looking at the debug files for the alignment it is running bwa aln and not bwa mem, though I didn't change anything else in the juicer.sh script to tell it to do short read alignment. Is this normal?

In case related to the version of bash I am running:

GNU bash, version 4.1.2(1)-release (x86_64-redhat-linux-gnu)
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

[imachol]

The check is working now, but is actually opposite to what you need -

try [ ! -z ${shortread+x} ] instead.

-v will return 1 if variable is unset, and 0 if it is set.

-v is only supported in version > 4.2, so I really recommend upgrading, or setting the value explicitly.

Ido

[keagen]

Great! Yes, it's working now. Thanks for all your help!

Kyle