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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 phage signal in output VIRsorter #26

Closed miasungeunlee closed 6 years ago

miasungeunlee commented 6 years ago

Dear Roux,

I'm currently working on soil viruses and i got illumina metagenomic data from my soil samples (DNA-SIP data). The number of obtained reads is quite good (around 200, 000 - 600, 000 reads after quality filtering). I used firstly Diamond (Blastx using viral protein database uploaded from NCBI) to see if the sequences contain the viral sequences. And i found the sequences matched with some viruses. However, when i used the Virsorter (on Cyverse with ID: mia), there was no phage signal in output VIRsorter file (/iplant/home/mia/analyses/M54_20180228-2018-02-28-14-08-00.0). In Cyverse, there was no error message which means the Virsorter worked well? Do you think what is a problem ??

I tried to run also on my computer, there was an error message : Cannot find mga_linux_ia64 Error: Failed to open sequence file /Users/leesungeun/Desktop/Output_virsorter/fasta/VIRSorter_prots.fasta for reading Error: Failed to open sequence file /Users/leesungeun/Desktop/Output_virsorter/fasta/VIRSorter_prots.fasta for reading Error: Failed to open sequence file /Users/leesungeun/Desktop/Output_virsorter/fasta/VIRSorter_prots.fasta for reading Command line argument error: Argument "query". File is not accessible: `/Users/leesungeun/Desktop/Output_virsorter/fasta/VIRSorter_prots.fasta' Can't open '/Users/leesungeun/Desktop/Output_virsorter/fasta/VIRSorter_circu.list' for reading: 'No such file or directory' at /Users/leesungeun/miniconda/envs/virsorter/bin/Scripts/Step_2_merge_contigs_annotation.pl line 39 Can't open '/Users/leesungeun/Desktop/Output_virsorter/VIRSorter_affi-contigs.csv' for reading: 'No such file or directory' at /Users/leesungeun/miniconda/envs/virsorter/bin/Scripts/Step_3_highlight_phage_signal.pl line 48 Can't open '/Users/leesungeun/Desktop/Output_virsorter/VIRSorter_phage-signal.csv' for reading: 'No such file or directory' at /Users/leesungeun/miniconda/envs/virsorter/bin/Scripts/Step_4_summarize_phage_signal.pl line 83

Your help is really appreciated :) Best wishes LEE

simroux commented 6 years ago

Dear Lee,

You mention a tblastx on your reads, did you assemble these reads into contigs before running VirSorter ? VirSorter is unfortunately not able to process reads, and can only work with larger contigs (ideally 10kb and more).

miasungeunlee commented 6 years ago

Thanks a lot for your reply :) I didn't use assembled reads. I'll try again with the contigs. It seems when i assembled my reads (from Miseq V3 2*300 bp) into contigs by SPAdes, i got the contig size less than 10kb... But i'll try again :)

Thanks