Errors running from dockerhub

[blue-moon22]

Hi there,

I'm getting errors running VirSorter. I run: docker run -v /home/vicky/Downloads/virsorter-data:/data -v /home/vicky/virsorter-run:/wdir --rm discoenv/virsorter:v1.0.3 --db 1 --fna /wdir/SRS013947_renamed_genes.fna

In the Step 5, I get this output: Step 5 : /usr/local/bin/Scripts/Step_5_get_phage_fasta-gb.pl VIRSorter >> /root/log_out 2>> /root/log_err

Cleaning the output directory rm -r r_0/db : mv: cannot stat 'formatdb.log': No such file or directory

In the Virsorter_stderr_log: Can't open 'Contigs_prots_vs_Phage_Gene_unclustered.tab' for reading: 'No such file or directory' at /usr/local/bin/Scripts/Step_2_merge_contigs_annotation.pl line 79 Can't open 'VIRSorter_affi-contigs.csv' for reading: 'No such file or directory' at /usr/local/bin/Scripts/Step_3_highlight_phage_signal.pl line 43 Can't open 'VIRSorter_phage-signal.csv' for reading: 'No such file or directory' at /usr/local/bin/Scripts/Step_4_summarize_phage_signal.pl line 83

My Metric_files and Predicted_viral_sequences folders, and VIRSorter_global_phage_signal.csv file are empty.

What have I missed?

Thanks!

[simroux]

Hi, Could you share the content of the log_out and log_err from VirSorter ? From what I see here, one guess might be that you are trying to run VirSorter on individual genes and not on contigs ? VirSorter requires at least 2 ORFs predicted on each input sequence, and if no sequence get through this first screen, you would get similar errors (i.e. empty files).

Best, Simon