simroux
commented
6 years ago 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
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_stderrlog: 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!