Question: Issues with running trinity on cluster
gravatar for dcole
3.2 years ago by
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,

(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/ line 758.
Error, cmd: /lustre/jasper/software6/trinity/trinityrnaseq-Trinity-v2.4.0/util/ --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 • 1.3k views
ADD COMMENTlink modified 3.2 years ago by genomax84k • written 3.2 years 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 3.2 years ago • written 3.2 years ago by genomax84k

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 3.2 years ago by dcole0
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