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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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please check external command status #56

Open EricDeveaud opened 4 years ago

EricDeveaud commented 4 years ago

Hello,

when running an external command it is a good practice to check the exit status of this one.

simple example. remove mga from your path and start wrapper_phage_contigs_sorter_iPlant.pl in an emptty location.it will ends with exit status 0. BUT Step_1_contigs_cleaning_and_gene_prediction.pl died because of no mga found.

so following hmmsearch command fail with 

Error: Failed to open sequence file `pwd`/virsorter-out/fasta/VIRSorter_prots.fasta for reading

and so on ...

can we consider the final results as accurate ?

Eric

simroux commented 4 years ago

Hi Eric, Thanks for the suggestion ! Since there is no support for the development of VirSorter, I can not commit on any timeline for when I will be able to implement them, but I'll certainly go through these as soon as I have some time to spend on VirSorter !

Best, Simon