Left read files: $VAR1 = [
          '/gscratch/srlab/sr320/data/NR021_R1_comb.fastq'
        ];
Right read files: $VAR1 = [
          '/gscratch/srlab/sr320/data/NR021_R1_comb.fastq'
        ];
Trinity version: Trinity-v2.4.0
-ERROR: couldn't run the network check to confirm latest Trinity software version.

which: no bowtie2 in (/gscratch/srlab/programs/trinity/trinity-plugins/BIN:/sw/local/bin:/usr/lib64/qt-3.3/bin:/sw/modules-1.775/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lusers/sr320/bin)
which: no bowtie2-build in (/gscratch/srlab/programs/trinity/trinity-plugins/BIN:/sw/local/bin:/usr/lib64/qt-3.3/bin:/sw/modules-1.775/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lusers/sr320/bin)
Error, cannot find path to bowtie2 () or bowtie2-build (), which is now needed as part of Chrysalis' read scaffolding step.  If you should choose to not run bowtie, include the --no_bowtie in your Trinity command.