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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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No sequences in Predicted_viral_sequences/ files #92

Open emily-ap opened 3 months ago

emily-ap commented 3 months ago

Hi, I've been trying to run VirSorter now and troubleshooting some, but I can't figure out why I'm not getting my viral sequences in my output. When I look in logs/err it's empty, the logs/out looks like this: 

/home/eja/VIRSorted/VirSorter/Scripts/Step_4_summarize_phage_signal.pl ../Teso_VS/VIRSorter_affi-contigs.csv ../Teso_VS/VIRSorter_phage-signal.csv ../Teso_VS/VIRSorter_global-phage-signal.csv ../Teso_VS/VIRSorter_new_prot_list.csv
No new prots, no list
/home/eja/VIRSorted/VirSorter/Scripts/Step_5_get_phage_fasta-gb.pl VIRSorter ../Teso_VS
Code VIRSorter
The sequences will be put in:
 - ../Teso_VS/Predicted_viral_sequences/VIRSorter_cat-1.fasta
 - ../Teso_VS/Predicted_viral_sequences/VIRSorter_cat-2.fasta
 - ../Teso_VS/Predicted_viral_sequences/VIRSorter_cat-3.fasta
 - ../Teso_VS/Predicted_viral_sequences/VIRSorter_prophages_cat-4.fasta
 - ../Teso_VS/Predicted_viral_sequences/VIRSorter_prophages_cat-5.fasta
 - ../Teso_VS/Predicted_viral_sequences/VIRSorter_prophages_cat-6.fasta
Checking '../Teso_VS/VIRSorter_phage-signal.csv'
VIRSorter       0       0       0       0       0       0

And my .fasta sequences exist in the Predicted_viral_sequences/ directory, they're just completely empty. The --no_c option hasn't helped here and I've reinstalled everything multiple times. Thank you for any help you can provide!

simroux commented 3 months ago

Hi ! Can you confirm that there were some viral sequences predicted (i.e. "global_phage_signal" is not empty ? ). Now that being said, VirSorter1 is quite outdated at this point, and I would recommend switching to e.g. geNomad instead (https://portal.nersc.gov/genomad/index.html) for better results.

Best, Simon

emily-ap commented 3 months ago

Hi Simon, yes there were. viral sequences in "global_phage"signal". And that makes sense (geNomad is great I've used it before!), we just needed virsorter for DRAMv because it requires the output.

simroux commented 3 months ago

Oh right, then here's some good news: we have a new pipeline called MVP that performs geNomad + CheckV prediction, and then prepares the input file for DRAM :-) You can try it out here https://gitlab.com/ccoclet/mvp/ , it's pretty new still so let us know if it doesn't work for you, but it'll likely be easier than running (and troubleshooting) VirSorter1 !

emily-ap commented 3 months ago

Oh great, I'll go ahead with that then! Thank you!