Question: Issues with running trinity on cluster
0
gravatar for dcole
8 months ago by
dcole0
dcole0 wrote:

Hello, I'm trying to run Trinity Denovo assembler for some RNA-seq analysis. I'm running this on a cluster. It returned the following error to me,

Jellyfish
(building a k-mer catalog from reads)

CMD finished (0 seconds)
CMD: /lustre/jasper/software6/trinity/trinityrnaseq-Trinity-v2.4.0/util/..//trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 100000000  both.fa
Error, cmd: /lustre/jasper/software6/trinity/trinityrnaseq-Trinity-v2.4.0/util/..//trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 100000000  both.fa died with ret 9 at /lustre/jasper/software6/trinity/trinityrnaseq-Trinity-v2.4.0/util/insilico_read_normalization.pl line 758.
Error, cmd: /lustre/jasper/software6/trinity/trinityrnaseq-Trinity-v2.4.0/util/insilico_read_normalization.pl --seqType fq --JM 50G  --max_cov 50 --CPU 2 --output /lustre/home/dcole/trinityassembly/insilico_read_normalization   --max_pct_stdev 10000  --SS_lib_type FR  --left /home/dcole/PostTrim/allsampleF.fastq.gz --right /home/dcole/PostTrim/allsampleR.fastq.gz --pairs_together --PARALLEL_STATS   died with ret 512 at /global/software/trinity/trinityrnaseq-Trinity-v2.4.0/Trinity line 2462.

Any ideas with what happened? I was not involved with the installation of Trinity on the cluster so I can't provide any info about whether this was done correctly or not, I assume it was though. Thanks!

rna-seq • 344 views
ADD COMMENTlink modified 8 months ago by genomax39k • written 8 months ago by dcole0

I was going to ask if this install is known to work (thank you for addressing that). If there is a test data set that is included in trinity then I suggest you try running that first to make sure things look sane. What kind of job scheduler are you using? The info you have posted does not seem to give a useful clue.

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax39k

I am not aware of any test data, but this is my first run through of RNA-seq analysis so I am not entirely familiar with everything. The cluster system uses TORQUE for resource managing and Moab for scheduling all batch jobs.

ADD REPLYlink written 8 months ago by dcole0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 957 users visited in the last hour