Question: Trinity run failed at start- please help
0
gravatar for gg832
4 months ago by
gg83210
gg83210 wrote:

Hello,

My Trinity run just failed with the error below. I'm trying to do a de novo assembly of paired-end RNAseq data. Any help with understanding this error and how I might correct it would be greatly appreciated!

Thanks,

Gia

Galaxy note:

workdir is /pylon5/mc48nsp/xcgalaxy/main_staging/15630112/working
Running Trinity from /local/1019704
slurmstepd: couldn't chdir to `(unreachable)/mc48nsp/xcgalaxy/main/pulsar/venv/src/pulsar': No such file or directory: going to /tmp instead
Trinity ver

Log data:

Trinity version: v2.2.0
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Wednesday, April 19, 2017: 20:23:50 CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 0
Wednesday, April 19, 2017: 20:23:50 CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 1
Wednesday, April 19, 2017: 20:23:50 CMD: mkdir -p /local/1019704/trinity_out_dir
Wednesday, April 19, 2017: 20:23:50 CMD: mkdir -p /local/1019704/trinity_out_dir/chrysalis


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

Converting input files. (in parallel)Wednesday, April 19, 2017: 20:23:50    CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415621.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /1 --to-fasta >> left.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415621.dat.readcount 
Wednesday, April 19, 2017: 20:23:50 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415622.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415622.dat.readcount 
Thread 1 terminated abnormally: Error, cmd: cat /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415621.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /1 --to-fasta >> left.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415621.dat.readcount  died with ret 256 at /opt/packages/trinity/2.2.0/Trinity line 2206.
Thread 2 terminated abnormally: Error, cmd: cat /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415622.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//15630112/inputs/dataset_19415622.dat.readcount  died with ret 256 at /opt/packages/trinity/2.2.0/Trinity line 2206.
Trinity run failed. Must investigate error above.
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson22k • written 4 months ago by gg83210
0
gravatar for Nate Coraor
4 months ago by
Nate Coraor3.0k
United States
Nate Coraor3.0k wrote:

Hi Gia,

This looks like a filesystem problem on Bridges, where Trinity runs. Could you try the job again and let us know if it encounters the same error please?

Thanks,
--nate

ADD COMMENTlink written 4 months ago by Nate Coraor3.0k

Hi Nate,

I submitted the job again ~11 hours ago. It's still waiting to run. I'm assuming it might be busy because it's just recently back up and running?

Thanks,

Gia

ADD REPLYlink written 4 months ago by gg83210
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Update:

Trinity was corrected again mid-day Friday 4/28/17 EST. Please re-run any jobs that failed.

If you have jobs that were started after that time, those will also need to be re-run (and the original grey jobs deleted/purged).

Sorry for the inconvenience, Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson22k
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