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.
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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