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vsearch error #191

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roo-weed opened this issue Feb 22, 2024 · 0 comments
Open

vsearch error #191

roo-weed opened this issue Feb 22, 2024 · 0 comments

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@roo-weed
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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!!

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