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Old 04-25-2014, 08:50 AM   #1
Tom2013
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Location: Canada

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Default trinity runing error

Hi everyone,

The RAM of my computer is 32GB and the size of my data is about 66GB. I set --JM 20G, --CPU. the Chrysalis process failed:

-------------------
---- Chrysalis ----
-------------------

mkdir: cannot create directory `/home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/chrysalis': File exists
###########################################################
## Running Bowtie to map fragment ends to Inchworm Contigs
## to use pairing info for Chrysalis' clustering
###############################################################

CMD: ln -sf /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/inchworm.K25.L25.DS.fa target.fa
CMD: bowtie-build -q target.fa target
CMD: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead -f target both.fa > bowtie.out
Reads file contained a pattern with more than 1024 sequence characters.
Please truncate reads and quality values and and re-run Bowtie.
Offending read: FCC327Identical(self):
terminate called after throwing an instance of 'int'
Aborted (core dumped)
COMMAND: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead -f target both.fa > bowtie.out
Died with exit code 34304
Exiting.
time(seconds) unlimited
file(blocks) unlimited
data(kbytes) unlimited
stack(kbytes) 8192
coredump(blocks) 0
memory(kbytes) unlimited
locked memory(kbytes) 64
process 256334
nofiles 1024
vmemory(kbytes) unlimited
locks unlimited

Error, the Chrysalis process failed:
Error, cmd: /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/Chrysalis/Chrysalis -i both.fa -iworm /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/inchworm.K25.L25.DS.fa -o /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/chrysalis -cpu 6 -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 -sort_buffer_size 20G -max_mem_reads 10000000 -paired -reads_for_pairs both.fa -butterfly /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/Butterfly/Butterfly.jar 2>&1 died with ret 65280 at Trinity.pl line 1793.

at Trinity.pl line 1322
main::run_chrysalis('/home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/A...', 'both.fa', 200, 500, undef, 'both.fa') called at Trinity.pl line 1136

Does anybody know how to solve the problem?

Thank you very much!

Tom
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Old 04-25-2014, 08:53 AM   #2
Tom2013
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Before I run all the sequences, I run only 1 sample (1 left file, 1 right file, 6.6GB in total) and it worked.
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Old 04-26-2014, 08:32 AM   #3
Thias
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I have not much experience in running Trinity, but from your logfile it seems that Bowtie existed abnormally and this also caused the Perl wrapper of Trinity to exit. Maybe you should have a closer look at the bowtie.out file, what caused the error.
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Old 05-08-2014, 09:48 AM   #4
Tom2013
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Does anybody have experience in running 70GB data in a computer with 32GB ram?
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