Error in the rRNAFinder.pl step

[etod5987]

Hi there, when I run metaERG I keep getting errors, and this latest one seems to be involving the creation of the arc.tblout file and the tRNA.masked.fna file. For some reason the file paths to generate these files have extra / and \ in them, including within file names like so:

metaERG/metaerg/bin/db/hmm/rna/arc.hmm

and

metaERG/output_test/tmp/metaerg.pl_04202021.tRNA.masked.fna

This results in steps further down the pipeline failing because they cannot find these output files.

Any suggestions on how to fix this error would be much appreciated.

[MatteoSchiavinato]

Maybe a stupid question but do you have all the necessary dependencies installed and in the $PATH?

[etod5987]

I am working on an institution HPC, I’ve tried to load in all the dependencies but I’m not sure if we have all of them installed. I’m going to be getting some help from the IT department to make sure we have everything required. Thanks for your reply!

…

________________________________ From: Matteo Schiavinato ***@***.***> Sent: Tuesday, 25 May 2021 11:41 PM To: xiaoli-dong/metaerg ***@***.***> Cc: Emma Charlotte Todd ***@***.***>; Author ***@***.***> Subject: Re: [xiaoli-dong/metaerg] Error in the rRNAFinder.pl step (#43) Maybe a stupid question but do you have all the necessary dependencies installed and in the $PATH? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#43 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATYEJPXLS4S7TPYKNJZ4IWTTPOSILANCNFSM43HF5KFQ>.

[nickp60]

can confirm this as well; I rebuilt the docker image using #38 and it worked as intended