Question: Problem in installing Trinity.
gravatar for majeedaasim
3.0 years ago by
United States
majeedaasim50 wrote:

I installed Trinity on my ubunto 16.04. When I test it on example data, Clustering, k-mer building, contig construction and clustering by Inchworm went fine but after that, it shows following error:

bowtie2-build: unrecognized option '--threads'
Bowtie 2 version 2.2.6 by Ben Langmead (,


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. ***


    -f                      reference files are Fasta (default)
    -c                      reference sequences given on cmd line (as
    --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 4 -o 3 /home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 /home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 
>  Error, cmd: bowtie2-build --threads 4 -o 3 /home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 /home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 1>/dev/null 2>tmp.25936.stderr died with ret 256 at /home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/PerlLib/ line 166. 
          Pipeliner::run(Pipeliner=HASH(0x19ca2c0)) called at ../../Trinity line 1827
main::run_chrysalis("/home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_dat"..., "/home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_dat"..., 200, 500, "RF", "/home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_dat"..., "/home/aasim/Aasim/bin/trinityrnaseq-Trinity-v2.5.0/sample_dat"...) called at ../../Trinity line 1667
    main::run_Trinity() called at ../../Trinity line 1320
    eval {...} called at ../../Trinity line 1319

Trinity run failed. Must investigate error above.

trinity software error • 1.6k views
ADD COMMENTlink modified 3.0 years ago by h.mon31k • written 3.0 years ago by majeedaasim50

Please provide all exact commands that got you to the point of this error.

ADD REPLYlink written 3.0 years ago by genomax91k
gravatar for h.mon
3.0 years ago by
h.mon31k wrote:

Update your Bowtie2 to a newer version. Checking my local Bowtie2 versions, there is no option --threads for bowtie2-build version 2.2.6, but --threads is available for bowtie2-build version 2.2.9.

edit: do not forget to include more details when asking for help, such as command-line used and software versions used.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by h.mon31k

I am using Trinity version 2.5.0 on Ubunto 16.4 I checked my bowtie2 version and it is up to date

bowtie2 --version /usr/bin/bowtie2-align-s version 2.2.6 64-bit Built on lgw01-12 Mon Dec 28 11:09:46 UTC 2015 Compiler: gcc version 5.3.1 20151219 (Ubuntu 5.3.1-4ubuntu1) Options: -O3 -m64 -msse2 -funroll-loops -g3 -Wl,-Bsymbolic-functions -Wl,-z,relro -DPOPCNT_CAPABILITY -DWITH_TBB Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

ADD REPLYlink written 3.0 years ago by majeedaasim50

The system-wide version of Bowtie2 is "up to date", but Ubuntu 16.04 is a long-term support release and software versions freeze and start to lag behind. You will have to download, install and add to your PATH a newer version of Bowtie2, luckily, the Bowtie2 devs offer a binary download:

mkdir ~/bin
mv bowtie2- ~/bin/Bowtie2-
export PATH=~/bin/Bowtie2-$PATH

Then you can run Trinity. If you want permanent the change in PATH, add export PATH=~/bin/Bowtie2-$PATH to your .bashrc.

ADD REPLYlink written 3.0 years ago by h.mon31k
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