please check external command status

[EricDeveaud]

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]

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