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/
