Hi all!
Apparently there are troubles with trinity, again.
The output of Trinity is an empty file so it doesn't produce an error. I paste here the first rows of the log in which there must be the error.
Trinity version: v2.2.0 -ERROR: couldn't run the network check to confirm latest Trinity software version.
Thursday, May 4, 2017: 07:08:57 CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 0 Thursday, May 4, 2017: 07:08:58 CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 1 Thursday, May 4, 2017: 07:09:00 CMD: mkdir -p /local/1111955/trinity_out_dir Thursday, May 4, 2017: 07:09:00 CMD: mkdir -p /local/1111955/trinity_out_dir/chrysalis
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
Thursday, May 4, 2017: 07:09:00 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//15746640/inputs/dataset_19815663.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta >> single.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//15746640/inputs/dataset_19815663.dat.readcount Trinity run failed. Must investigate error above.
The purpose of my the jobs is a 2nd round assembling (by pooling togheter several samples of the same condition) so I simply run trinity with the .fasta file generated by its output. Accordingly, I changed the parameters of the run (i.e. single end). Can I run trinity with .fasta file from Galaxy?
Anyone can help me?
Thank you,
Luca
Hi Luca,
I'll start a test trinity run to see if a generalized server issue is present. Please do the same (rerun as a first pass solution). Maybe also rerun a prior job that you know works if you have one. Reruns are quick to launch.
I'll also go into your account and examine the actual data to ensure there is not some input/format problem. Feedback soon! Jen, Galaxy team