Error during Inchworm process

[loeka vandenchrick]

Hello, 

My trinity keeps failing at the inchworm process even tho the jellyfish process is succesful. I am working with really large files of 1,8 TB. It keeps giving me this error: 

Error, cmd: /home/lvdschrick/miniconda3/envs/trinity_env/bin/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --DS  --keep_tmp_files  --num_threads 6  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /home/lvdschrick/RNA/data/combined_reads/trinity_out/inchworm.DS.fa.tmp died with ret 36608 No such file or directory at /home/lvdschrick/miniconda3/envs/trinity_env/bin/PerlLib/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x55f8df2894b0)) called at /home/lvdschrick/miniconda3/envs/trinity_env/bin/Trinity line 2729
eval {...} called at /home/lvdschrick/miniconda3/envs/trinity_env/bin/Trinity line 2719
main::run_inchworm("/home/lvdschrick/RNA/data/combined_reads/trinity_out/inchworm"..., "/home/lvdschrick/RNA/data/combined_reads/trinity_out/both.fa", undef, "", 25, 0) called at /home/lvdschrick/miniconda3/envs/trinity_env/bin/Trinity line 1836
main::run_Trinity() called at /home/lvdschrick/miniconda3/envs/trinity_env/bin/Trinity line 1500
eval {...} called at /home/lvdschrick/miniconda3/envs/trinity_env/bin/Trinity line 1499

If it indicates bad_alloc(), then Inchworm ran out of memory.  You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.

** The inchworm process failed.

The initial code i entered was this one: 

nohup Trinity --seqType fq --left /home/lvdschrick/RNA/data/combined_reads/combined_1_90.fq.gz --right /home/lvdschrick/RNA/data/combined_reads/combined_2_90.fq.gz --max_memory 500G --CPU 6 --no_normalize_reads --min_kmer_cov 2 --output /home/lvdschrick/RNA/data/combined_reads/trinity_out_retry2 --no_cleanup > /home/lvdschrick/RNA/data/combined_reads/trinity_retry2.log 2>&1 &

If anyone knows what I can do to fix this, would be greatly appreciated! 

Loeka

[Brian Haas]

Hi,

If it's running out of memory, increasing the --min_kmer_cov to 3 should help.

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas