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Old 06-13-2017, 12:00 PM   #1
M.Verma
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Location: Bangalore

Join Date: Jun 2012
Posts: 12
Default Trinity error

Hello,

I am trying to do assembly through Trinity but i am getting this error during Chrysalis running. PLease help me out to rectify this error.

Thank You


-----------------------------------------
--- Chrysalis: GraphFromFasta -----------
-- (cluster related inchworm contigs) ---
-----------------------------------------

-setting num threads to: 2
-running on 2 threads
GraphFromFasta: Reading file: /ddnB/work/mverma/New_Data/Tuu_Gia_M_fijiensis_24_hpi_trinity_output/inchworm.K25.L25.DS.fa
done!
Counting k-mers...
KmerAlignCore- Contigs: 1038967
done, assigning k-mers...
KmerAlignCore- Contigs: 1038967
done!
-setting omp for schedule chunksize to 5194 for 1038968 iworm contigs
Phase 1: Collecting candidate weldmers between iworm contig pairs sharing k-1mers
Processed: 99.9999 % of iworm contigs.

...done Phase 1. (447.19 seconds)
Captured: 1341537 weldmer candidates.
Setting up reads for streaming...
Identifying reads that support welding of iworm contigs...
Reads: (unknown count: streaming-mode)

Message from root@mike1 on <no tty> at 15:15 ...
User mverma process GraphFromFasta killed >30 min, using 3% of memory
EOF
sh: line 1: 36680 Killed /home/packages/bioinformatics/trinityrnaseq/2.0.6/Intel-13.0.0/Chrysalis/GraphFromFasta -i /ddnB/work/mverma/New_Data/Tuu_Gia_M_fijiensis_24_hpi_trinity_output/inchworm.K25.L25.DS.fa -r single.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 > /ddnB/work/mverma/New_Data/trinity_output/chrysalis/GraphFromIwormFasta.out
Trinity run failed. Must investigate error above.
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Old 06-14-2017, 05:45 PM   #2
neavemj
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Location: MA, USA

Join Date: Feb 2014
Posts: 58
Default

It sounds like your job was purposely cancelled after 30 minutes. This is probably because the server you are using has a job scheduling system, e.g., SLURM. With these systems, you need to write a shell script requesting a certain amount of memory and time, then your job will run when it gets to the top of the "queue".

Maybe you could email the administrator (Mike?) and ask how it works.

Good luck!

Matt.
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