This occurs when bzip2 is installed from defaults instead of conda-forge.
If you have Conda >= 4.0 this shouldn't happen as long as you install with
the right channel order e.g. `-c iuc -c bioconda -c conda-forge -c
defaults`. You should be able to fix this one with:

  conda install -n __trinity@2.4.0 -c conda-forge bzip2=1.0.6=1

--nate

On Thu, Mar 1, 2018 at 10:41 AM, Jochen Bick <jochen.b...@usys.ethz.ch>
wrote:

> Hej all,
>
> I'm also facing another problem which might be related to my previous
> error, when I run Trinity:
>
> samtools: error while loading shared libraries: libbz2.so.1.0: cannot
> open shared object file: No such file or directory
> samtools: error while loading shared libraries: libbz2.so.1.0: cannot
> open shared object file: No such file or directory
> Error outputting data
> Error: Encountered internal Bowtie 2 exception (#1)
> Command:
> /opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/bowtie2-align-s
> --wrapper basic-0 --local -k 2 --threads 5 -f --score-min G,46,0 -x
> /opt/galaxy/production/galaxy-dist/database/jobs_directory/
> 018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
> /opt/galaxy/production/galaxy-dist/database/jobs_directory/
> 018/18987/working/trinity_out_dir/both.fa
>
> (ERR): bowtie2-align exited with value 1
> Error, cmd: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 5
> -f --score-min G,46,0 -x
> /opt/galaxy/production/galaxy-dist/database/jobs_directory/
> 018/18987/working/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100
> /opt/galaxy/production/galaxy-dist/database/jobs_directory/
> 018/18987/working/trinity_out_dir/both.fa
>  | samtools view -@ 5 -F4 -Sb - | samtools sort -m 107374182 -@ 5 -no -
> - >
> /opt/galaxy/production/galaxy-dist/database/jobs_directory/
> 018/18987/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
>  2>tmp.54212.stderr died with ret 32512 at
> /opt/galaxy/production/_conda/envs/__trinity@2.4.0/opt/
> trinity-2.4.0/PerlLib/Pipeliner.pm
> line 166.
>         Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at
> /opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1750
>         main::run_chrysalis("/opt/galaxy/production/galaxy-dist/
> database/jobs_directory/01"..., "/opt/galaxy/production/
> galaxy-dist/database/jobs_directory/01"..., 200, 500, "RF",
> "/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...,
> "/opt/galaxy/production/galaxy-dist/database/jobs_directory/01"...)
> called at /opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity
> line 1595
>         main::run_Trinity() called at
> /opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1262
>         eval {...} called at
> /opt/galaxy/production/_conda/envs/__trinity@2.4.0/bin/Trinity line 1261
>
> Trinity run failed. Must investigate error above.
>
>
> has anyone got an idea?
>
> Cheers Jochen
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