Fatal Error: Exit Code 132 () Using VSearch:Search


#1

I am currently working on a galaxy workflow with illumina paired-end read data:
FastQC -> Trimmomatic -> Pear:Assemble Reads -> FASTQ to FASTA -> VSearch:Sorting (by abundance) -> VSearch:Clustering (Centroids) -> …

Intent:
I would like to use VSearch:Search to match my targeted amplicon (P. ganteri COI gene) to any found in the centroid file generated from clustering. The reference amplicons are contained in a FASTA uploaded from my computer. However, when I try to use the VSearch:Search tool with my previous centroid file output and my local query FASTA I keep getting an error.

Command Line reads:
vsearch --threads “${GALAXY_SLOTS:-4}” --notrunclabels --db “/galaxy-repl/main/files/029/076/dataset_29076608.dat” --dbmask “none” --id “0.5” --iddef “4” --qmask “none” --strand “plus” --usearch_global “/galaxy-repl/main/files/029/034/dataset_29034509.dat” --blast6out “/galaxy-repl/main/files/029/076/dataset_29076680.dat” --dbmatched “/galaxy-repl/main/files/029/076/dataset_29076679.dat” --dbnotmatched “None”

Tool Error Report shows:
Fatal error: Exit code 132 ()
vsearch v2.8.3_linux_x86_64, 125.7GB RAM, 32 cores

Reading file /galaxy-repl/main/files/029/076/dataset_29076608.dat 100%
1264 nt in 2 seqs, min 632, max 632, avg 632
/galaxy-repl/main/jobdir/021/904/21904040/tool_script.sh: line 25: 20461 Illegal instruction (core dumped) vsearch --threads “${GALAXY_SLOTS:-4}” --notrunclabels --db “/galaxy-repl/main/files/029/076/dataset_29076608.dat” --dbmask “none” --id “0.5” --iddef “4” --qmask “none” --strand “plus” --usearch_global “/galaxy-repl/main/files/029/034/dataset_29034509.dat” --blast6out “/galaxy-repl/main/files/029/076/dataset_29076680.dat” --dbmatched “/galaxy-repl/main/files/029/076/dataset_29076679.dat” --dbnotmatched “None”


#2

Update on this topic… If you currently need to use VSearch stick with one of the previous versions in the toolkit.

I have found that the current version of VSearch (v 2.8.3.0) is the issue here. Ran this exact workflow using VSearch: Search (v 1.9.7.0) in the galaxy toolkit and it preformed as expected. Other workflows that have previously preformed are also stalled out using the current version of VSearch. They all report the same error stemming from the tool_script.sh file at line 25.

Thanks for any time anyone placed into this issue!


#3

Hi, I found your reported bugs associated with this tool suite. The root cause/scope for the error is not yet known and we do not (yet) have any other reports of a problem. More feedback once the review is completed.

Thanks for posting the issue and your workaround!