Closed DanieleDeco closed 7 years ago
I randomly get this one as well.
Can't open '/wdir/input_contig.fna' for reading: 'No such file or directory' at /usr/local/bin/wrapper_phage_contigs_sorter_iPlant.pl line 148
Hi Daniele,
This looks like VirSorter having troubles reading your input files and/or writing in the working directory. Could there be some permission issues in /Users/daniele1/Desktop/VirSorter/virsorter-run ? Also, could you post here the content of /Users/daniele1/Desktop/VirSorter/virsorter-run and /Users/daniele1/Desktop/VirSorter/virsorter-run/fasta (or /Users/daniele1/Desktop/VirSorter/virsorter-run/Fasta_files/) after one of these failed runs ?
Hi Simon,
I solved the problem, I had to change the directory permission.
Many Thanks for your help.
Cheers Daniele
Great, happy that it's solved !
Hey,
I am trying to run my virome with VirSoter on my machine and I got few errors. Could you please take a look?
Many Thanks in advance.
Cheers Daniele
Run: docker run -v /Users/daniele1/Desktop/VirSorter/virsorter-data:/data -v /Users/daniele1/Desktop/VirSorter/virsorter-run:/wdir -w /wdir --rm discoenv/virsorter:v1.0.3 --db 2 --fna /wdir/input_contig.fna
Cleaning the output directory rm -r r_0/db : mv: cannot stat 'Contigs_prots_vs_PFAMa.tab': No such file or directory mv: cannot stat 'Contigs_prots_vs_PFAMa.out': No such file or directory mv: cannot stat 'Contigs_prots_vs_PFAMb.tab': No such file or directory mv: cannot stat 'Contigs_prots_vs_PFAMb.out': No such file or directory mv: cannot stat 'error.log': No such file or directory mv: cannot stat 'formatdb.log': No such file or directory mv: cannot stat 'VIRSorter_affi-contigs.csv': No such file or directory mv: cannot stat 'VIRSorter_affi-contigs.refs': No such file or directory mv: cannot stat 'VIRSorter_phage-signal.csv': No such file or directory
The log file:
Error: Failed to open sequence file /wdir/fasta/VIRSorter_prots.fasta for reading
Error: Failed to open sequence file /wdir/fasta/VIRSorter_prots.fasta for reading
Error: Failed to open sequence file /wdir/fasta/VIRSorter_prots.fasta for reading
[blastall] FATAL ERROR: blast: Unable to open input file /wdir/fasta/VIRSorter_prots.fasta
Can't open '/wdir/fasta/VIRSorter_circu.list' for reading: 'No such file or directory' at /usr/local/bin/Scripts/Step_2_merge_contigs_annotation.pl line 39 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