Hello,
Thanks in advance for any help or consideration!
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. The reference amplicons are contained in a FASTA uploaded from my computer. I have uploaded the file and normalized it to a line-length of 80 for standardization. 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.
I have tried editing the input file to contain no special characters (only ones were “_”) and reducing the query FASTA to just one 400 bp sequence and even switching around the inputs. I am guessing there is something simple I have missed but have found nothing in the manual on the VSearch website.
Command Line reads:
vsearch --threads “${GALAXY_SLOTS:-4}” --notrunclabels --db “/galaxy-repl/main/files/029/076/dataset_29076608.dat” --dbmask “none” --id “0.5” --iddef “4” --qmask “none” --strand “plus” --usearch_global “/galaxy-repl/main/files/029/034/dataset_29034509.dat” --blast6out “/galaxy-repl/main/files/029/076/dataset_29076680.dat” --dbmatched “/galaxy-repl/main/files/029/076/dataset_29076679.dat” --dbnotmatched “None”
Tool Error Report shows:
Fatal error: Exit code 132 ()
vsearch v2.8.3_linux_x86_64, 125.7GB RAM, 32 cores
vsearch v2.8.3_linux_x86_64, 125.7GB RAM, 32 cores
Reading file /galaxy-repl/main/files/029/076/dataset_29076608.dat 100%
1264 nt in 2 seqs, min 632, max 632, avg 632
/galaxy-repl/main/jobdir/021/904/21904040/tool_script.sh: line 25: 20461 Illegal instruction (core dumped) vsearch --threads “${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”
Not sure what the “Illegal instruction” is in line 25 and cannot get additional information to troubleshoot what I have done wrong… maybe someone can give me an idea?