Trinity-v2.5.1 assembly generating bowtie 2 error
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6.6 years ago
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Hi I am running Trinity (Trinity-v2.5.1) invoking the following command :

Trinity --seqType fq --max_memory 100G --right /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897_1.fastq --left /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897_2.fastq --CPU 16 --output /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897-trinity-output

This however generates the following error posted below. Could someone please help me resolve this problem. Thanks!

Error:

put/chrysalis/inchworm.K25.L25.DS.fa.min100 /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897-trinity-output/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null
bowtie2-build: unrecognized option '--threads'
Bowtie 2 version 2.2.4 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: bowtie2-build [options]* <reference_in> <bt2_index_base>
    reference_in            comma-separated list of files with ref sequences
    bt2_index_base          write bt2 data to files with this dir/basename
*** Bowtie 2 indexes work only with v2 (not v1).  Likewise for v1 indexes. ***
Options:
    -f                      reference files are Fasta (default)
    -c                      reference sequences given on cmd line (as
                            <reference_in>)
    --large-index           force generated index to be 'large', even if ref
                            has fewer than 4 billion nucleotides
    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting
    -p/--packed             use packed strings internally; slower, less memory
    --bmax <int>            max bucket sz for blockwise suffix-array builder
    --bmaxdivn <int>        max bucket sz as divisor of ref len (default: 4)
    --dcv <int>             diff-cover period for blockwise (default: 1024)
    --nodc                  disable diff-cover (algorithm becomes quadratic)
    -r/--noref              don't build .3/.4 index files
    -3/--justref            just build .3/.4 index files
    -o/--offrate <int>      SA is sampled every 2^<int> BWT chars (default: 5)
    -t/--ftabchars <int>    # of chars consumed in initial lookup (default: 10)
    --seed <int>            seed for random number generator
    -q/--quiet              verbose output (for debugging)
    -h/--help               print detailed description of tool and its options
    --usage                 print this usage message
    --version               print version information and quit
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 --threads 16 -o 3 /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897-trinity-output/chrysalis/inchworm.K25.L25.DS.fa.min100 /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897-trinity-output/chrysalis/inchworm.K25.L25.DS.fa.min100 
Error, cmd: bowtie2-build --threads 16 -o 3 /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897-trinity-output/chrysalis/inchworm.K25.L25.DS.fa.min100 /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897-trinity-output/chrysalis/inchworm.K25.L25.DS.fa.min100 1>/dev/null 2>tmp.138488.stderr died with ret 256 at /home/owner/Desktop/executables/trinityrnaseq-Trinity-v2.5.1/PerlLib/Pipeliner.pm line 166.
    Pipeliner::run('Pipeliner=HASH(0x229eee8)') called at /home/owner/Desktop/executables/trinityrnaseq-Trinity-v2.5.1//Trinity line 1827
    main::run_chrysalis('/media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal...', '/media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal...', 200, 500, undef, '/media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal...', '/media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal...') called at /home/owner/Desktop/executables/trinityrnaseq-Trinity-v2.5.1//Trinity line 1667
    main::run_Trinity() called at /home/owner/Desktop/executables/trinityrnaseq-Trinity-v2.5.1//Trinity line 1320
    eval {...} called at /home/owner/Desktop/executables/trinityrnaseq-Trinity-v2.5.1//Trinity line 1319

Trinity run failed. Must investigate error above.
rnaseq trinity • 3.0k views
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