ESPRESSO_Q.pl can't open -L

[humblebeebio]

Hello,

I am trying to run the ESPRESSO_Q.pl script but I am getting the following error:

can't open -L: No such file or directory at {path to root}/espresso/src/ESPRESSO_Q_Thread.pm line 18.
Compilation failed in require at {path to root}/espresso/src/ESPRESSO_Q.pl line 10.
BEGIN failed--compilation aborted at {path to root}/espresso/src/ESPRESSO_Q.pl line 10.

I checked the updated tsv file and it appears to be in the correct format (tab delimited with the correct number of columns and correct column values).

I suspect there is an issue with the ESPRESSO_Q.pl script locating the ESPRESSO_Q_Thread.pm script. What is your proposed installation method without the Snakemake script?

I tried adding the src directory to my path but the bash interpreter can't execute the script without a perl header (adding these didn't seem to fix the issue).

All the other scripts ran successfully by executing them with perl and providing the full path to source.

Thanks!

[EricKutschera]

It looks like that error can happen if ESPRESSO_Q.pl is called with only the -L argument like: perl ESPRESSO_Q.pl -L /path/to/samples.tsv.updated

The issue is that ESPRESSO_Q_Thread.pm is used in two ways. As an import: https://github.com/Xinglab/espresso/blob/v1.3.0-beta/src/ESPRESSO_Q.pl#L10 As a script: https://github.com/Xinglab/espresso/blob/v1.3.0-beta/src/ESPRESSO_Q.pl#L550

It tries to figure out if it is an import by checking for command line arguments: https://github.com/Xinglab/espresso/blob/v1.3.0-beta/src/ESPRESSO_Q_Thread.pm#L7

That is probably not the correct way for a module to figure out if it is being imported. For now you should be able to resolve the error by providing any additional argument to ESPRESSO_Q.pl for example specify the number of threads to be 5 (the default): perl ESPRESSO_Q.pl -L /path/to/samples.tsv.updated -T 5

[EricKutschera]

ESPRESSO v1.3.1 includes a fix for this error