Question: Trinity is not working..again?
gravatar for luca.marisaldi
12 months ago by
luca.marisaldi30 wrote:

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,


assembly trinity rna-seq • 367 views
ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson25k • written 12 months ago by luca.marisaldi30

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

ADD REPLYlink written 12 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Luca,

The reads are not NGS RNA-seq reads, but assembled reads. This may be the root of the problem.

I tested re-running your job and it failed. Several other Trinity test runs were successful.

Your reads are not that long in length and you did pick single-end sequencing on the tool form. There may be a way to format the data so that the tool will accept it. I am testing out some potential workarounds and will reply if I can get one to work.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 12 months ago by Jennifer Hillman Jackson25k
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