Trinity Help

[dmacmillan]

So I ran trinity, but I am experiencing this error:

Error, the Chrysalis process failed:
Error, cmd: /projects/dmacmillanprj2/assembly/trinityrnaseq_r2012-04-27/Chrysalis/Chrysalis -i both.fa -iworm /projects/dmacmillanprj2/assembly/testing_trinity/output/inchworm.K25.L25.fa.clipped.fa -o chrysalis -cpu 20 -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 20000000 -max_mem_reads 1000000 -strand 1 -paired -butterfly /projects/dmacmillanprj2/assembly/trinityrnaseq_r2012-04-27/Butterfly/Butterfly.jar 2>&1 died with ret 65280 at trinityrnaseq_r2012-04-27/Trinity.pl line 1142.

In nearly all cases, this is related to not having the stacksize set to unlimited, a prerequisite to running Trinity.
Please visit:

http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_E

for details.



This is my command:

perl trinityrnaseq_r2012-04-27/Trinity.pl --seqType fq --kmer_method meryl --left testing_trinity/SRR097928_1.fastq --right testing_trinity/SRR097928_2.fastq --output testing_trinity/output --CPU 20 --SS_lib_type RF --jaccard_clip --bfly_opts "--edge-thr=0.05 --compatible_path_extension"

[westerman]

And???

Did you go the the FAQ and follow what it says there in regards to the stack size?

[dmacmillan]

Yes sorry I forgot to mention I tried the obvious, setting the stacksize to unlimited did not solve the problem.

[westerman]

OK. I see nothing obviously wrong. Best is to post to the user's mailing list. They are very active there.

[email protected]

[pbluescript]

I had a similar error that turned out to be due to not enough RAM. I switched from a 24GB RAM machine to a 96 GB RAM machine and it worked fine. How much RAM are you using?

[pbluescript]

OK. I see nothing obviously wrong. Best is to post to the user's mailing list. They are very active there.

[email protected]

I agree with using the mailing list. The developers are very responsive too.