Question: Trinity don't work during inchworm step
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gravatar for park.seojeong2
2.2 years ago by
park.seojeong20 wrote:

Hi.

I'm assembling pair-end RNA-seq using Trinity v2.4.0. Other options : --seqType fq --max_memory 30G --samples_file WT_samples.txt --CPU 16 --output WT_Trinity_out --full_cleanup

I have some problem during inchworm. When i'm running trinity, it don't work during inchworm step (just stop) and cannot see any error command.


--------------- Inchworm ---------------------

-- (Linear contig construction from k-mers) --

  • Running CMD: /home/ngan/.compiz/Installed_software/Trinity/trinityrnaseq-Trinity-v2.4.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --num_threads 6 --PARALLEL_IWORM > /drive2/Seojeong/kim/2.trinity/WT/WT_Trinity_out/inchworm.K25.L25.DS.fa.tmp

It don't say any error command and just stop. so i cannot know what's the problem. how can i solve this problem?

assembly • 664 views
ADD COMMENTlink written 2.2 years ago by park.seojeong20

did you solve this problem?

ADD REPLYlink written 25 days ago by kanchaan360
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