Error at Inchworm during running Trinity

Question

[snar86]

Hello,

I ran Trinity with this command

Trinity --seqType fq --max_memory 20G --left 2025-bark-1b_R1.fastq --right 2025-bark-1b_R2.fastq --SS_lib_type RF --CPU 8

but i got this error:

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

* Running CMD: /home/snar/tools/trinityrnaseq-2.2.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  > /home/snar/trial/trinity_out_dir/inchworm.K25.L25.fa.tmp
sh: line 1:  6941 Aborted                 /home/snar/tools/trinityrnaseq-2.2.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --num_threads 6 --PARALLEL_IWORM > /home/snar/trial/trinity_out_dir/inchworm.K25.L25.fa.tmp 2> tmp.6104.stderr
Kmer length set to: 25
Min assembly length set to: 25
Monitor turned on, set to: 1
setting number of threads to: 6
-setting parallel iworm mode.
-reading Kmer occurrences...
 [239M] Kmers parsed.     
 done parsing 239420656 Kmers, 239420656 added, taking 367 seconds.

TIMING KMER_DB_BUILDING 367 s.
Pruning kmers (min_kmer_count=1 min_any_entropy=0 min_ratio_non_error=0.05)
Pruned 3528884 kmers from catalog.
    Pruning time: 313 seconds = 5.21667 minutes.


TIMING PRUNING 313 s.
-populating the kmer seed candidate list.
Kcounter hash size: 239420656
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Error, cmd: /home/snar/tools/trinityrnaseq-2.2.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  > /home/snar/trial/trinity_out_dir/inchworm.K25.L25.fa.tmp 2>tmp.6104.stderr died with ret 34304 at /home/snar/tools/trinityrnaseq-2.2.0/PerlLib/Pipeliner.pm line 102
    Pipeliner::run('Pipeliner=HASH(0x24a4598)') called at /home/snar/tools/trinityrnaseq-2.2.0/Trinity line 2058
    eval {...} called at /home/snar/tools/trinityrnaseq-2.2.0/Trinity line 2053
    main::run_inchworm('/home/snar/trial/trinity_out_dir/inchworm.K25.L25.fa', 'both.fa', 'RF', '') called at /home/snar/tools/trinityrnaseq-2.2.0/Trinity line 1428
    main::run_Trinity() called at /home/snar/tools/trinityrnaseq-2.2.0/Trinity line 1209
    eval {...} called at /home/snar/tools/trinityrnaseq-2.2.0/Trinity line 1208

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.[snar@hypercube trial]$

Why is this happening? Can anyone help me?

Thank you

[Damian Kao]

You've kinda answered your own question:

You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.

[snar86]

Actually this verse below included in the error that i copied.

"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.[snar@hypercube trial]$ "

I do not know why they are out of the box. I already run it in a server. That's why I felt weird why it ran out of memory.

Answer 1

[Antonio R. Franco]

You have several choices when getting this error

1. Do what Damian and the own Trinity is asking: reduce the size of your data set or run it in a server with more memory available

2. Try to use Trinity with normalization of data, which reduces the amount of your data set. See THIS WEB PAGE for more information

3. Use the Galaxy Trinity service that is freely available at the Indiana University. You need to open an account, though. Last time I used it, I was able to use it with 240Gb of available RAM

[st.ph.n]

I agree with Antonio. If you're going to try to assemble these data on your current machine, use the in silico read normalization parameter. This will reduce the memory usage, and speed up the runtime. Did you combine many samples to make the read pairs for input to Trinity?

[snar86]

Thank you for these choices you've given, sir. I will try to do what you've suggested here. Thank you.

Answer 2

[snar86]

Actually this verse below included in the error that i copied.

"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.[snar@hypercube trial]$ "

I do not know why they are out of the box.

Thank you for all the answers given. Actually, I already run it in a server. That's why I felt weird why it ran out of memory.

For this process, I did not combine many samples to make the read pairs for input to Trinity. Only one for left and one for right.

I will try to use in silico read normalization parameter to solve this although I run it in a server.

May I know, how long is actually the assembly process usually take? This is because I had tried run it using the combined many samples data before this but still not finished even after 2 weeks. The process is static at Inchworm. So, that is why I tried again with uncombined data (for trial). But this error occurred. This is my first time doing this process. I am a newbie. Hope anyone can help. Thank you so much.