search

mgimenez720 / plaSquid

Nextflow pipeline for plasmid detection and classification from metagenomic data
GNU General Public License v3.0
7 stars 1 forks source link

ERROR ~ Error executing process > 'SetPlsdb:FormtPLSDB' #18

Closed macarenaalga closed 1 year ago

macarenaalga commented 1 year ago

Hello! I was trying to run plaSquid, and I encountered the following error, both with the test file and a personal one:

`ERROR ~ Error executing process > 'SetPlsdb:FormtPLSDB'

Caused by: Process SetPlsdb:FormtPLSDB terminated with an error exit status (137)

Command executed:

minimap2 -d plsdb.mmi plsdb.fna cp plsdb.mmi /home/quimica/Descargas/plaSquid/plsdb.mmi

Command exit status: 137

Command output: (empty)

Command error: .command.sh: línea 2: 28242 Terminado (killed) minimap2 -d plsdb.mmi plsdb.fna

Work dir: /home/quimica/Descargas/plaSquid/work/ee/91d92526805223fb350ecc3d088c31

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

`

Upon reviewing the generated output, I noticed that while the plsdb.fna file was created, the plsdb.mmi file has 0 bytes, and I believe this is the cause of the error. I'm not sure if you could provide guidance on how to resolve this issue. Regards, Macarena.

mgimenez720 commented 1 year ago

Hello, thank you Macarena for trying plaSquid and giving your feedback.

There was a bug in the conda definition file, bzip2 is needed to decompress plsdb database for building minimap2 database. This is already corrected and hope that now you can use it with no problems.

When downloading plsdb it is also important to check stable internet connection and to have ~10Gb of free space in the disk, in order to download and format the database correctly.