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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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vsearch error #191

Open roo-weed opened 7 months ago

roo-weed commented 7 months ago

Hi! Thanks for developing this tool!

I'm getting a somewhat mysterious error that I'm hoping to get some help with! The error occurred on the following subcommand:

running subcommand:
       /bioware/vsearch-2.4.0/bin/vsearch -usearch_global
       11M.all.final.fasta -id 0.7 -userout 11M.all.vsearch.csv
       -userfields
       query+target+id+alnlen+evalue+id3+qs+pairs+gaps+mism+ids
       -threads 40 --strand plus --notrunclabels -notmatched
       11M.all.final.phyloFlash.notmatched.fa -dbmatched
       11M.all.final.phyloFlash.dbhits.fa -db
       /automounts/workspace/workspace/rweed/Beacon/phyloFlash/138.1/SILVA_SSU.noLSU.masked.trimmed.udb
       >11M.all.vsearch.out 2>&1
Error:
FATAL: Tool execution failed!.
       Error was '' and return code '256'
       Check log file 11M.all.vsearch.out
       Check error log file &1
       Aborting.

Here is what 11M.all.vsearch.out looks like: Fatal error: File type not recognized. It looks like this step should just be inputting a fasta, so it's odd that it's telling me that it doesn't recognize the file type. Any advice would be much appreciated!!