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 [email protected] -c conda-forge bzip2=1.0.6=1 --nate On Thu, Mar 1, 2018 at 10:41 AM, Jochen Bick <[email protected]> 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/[email protected]/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/[email protected]/opt/ > trinity-2.4.0/PerlLib/Pipeliner.pm > line 166. > Pipeliner::run(Pipeliner=HASH(0xd8f630)) called at > /opt/galaxy/production/_conda/envs/[email protected]/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/[email protected]/bin/Trinity > line 1595 > main::run_Trinity() called at > /opt/galaxy/production/_conda/envs/[email protected]/bin/Trinity line 1262 > eval {...} called at > /opt/galaxy/production/_conda/envs/[email protected]/bin/Trinity line 1261 > > Trinity run failed. Must investigate error above. > > > has anyone got an idea? > > Cheers Jochen > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ >
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