Question: Probem with the Trinity de-novo assembly for big dataset (128GB)
gravatar for tcf.hcdg
6 months ago by
tcf.hcdg0 wrote:

I had 48 paired end samples, I concatinae all the 24 forward and reverse paired separately and tried to do denovo assembly for concatinated forward read (64GB) and reverse read (64GB).

Trinity run failed with the fllowing error.

is it due to the concatination or something else, Please suggest how to proceed?

[2018-05-24 05:27:39.893] [jointLog] [warning] Salmon was only able to assign 0 fragments to transcripts in the index, but the minimum number of required assigned fragments (--minAssignedFrags) was 1. This could be indicative of a mismatch between the reference and sample, or a very bad sample. You can change the --minAssignedFrags parameter to force Salmon to quantify with fewer assigned fragments (must have at least 1).

Error, cmd:
salmon --no-version-check quant -i /N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa.out/Trinity.fasta.tmp.salmon.idx -l U -r /N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa.out/single.fa -o salmon_outdir -p 1 --minAssignedFrags 1 
 died with ret (256) at /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts/../../PerlLib/ line 19.

Process_cmd::process_cmd("salmon --no-version-check quant -i /N/dc2/scratch/trinity/job"...) called at /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts/ line 26

Trinity run failed. Must investigate error above.

warning, cmd: /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/util/support_scripts/../../Trinity --single "/N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa" --output "/N/dc2/scratch/trinity/job_working_directory/021/21127/working/trinity_out_dir/read_partitions/Fb_0/CBin_294/c29490.trinity.reads.fa.out" --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup   failed with ret: 512, going to retry.

succeeded(0), failed(1) 50% completed.
succeeded(0), failed(2) 100% completed.

We are sorry, commands in file: [FailedCommands] failed. :-(

Error, cmd: /gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 8 -v -shuffle  died with ret 256 at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 2581.
    main::process_cmd("/gpfs/hps/soft/rhel7/trinityrnaseq/2.6.6/trinity-plugins/BIN/"...) called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 3244
    main::run_partitioned_cmds("recursive_trinity.cmds") called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 2239
    main::run_recursive_trinity("/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"...) called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 2001
    main::run_chrysalis("/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"..., "/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"..., 200, 500, undef, "/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"..., "/N/dc2/scratch/trinity/job_working_directory/021/21127/workin"...) called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 1664
    main::run_Trinity() called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 1317
    eval {...} called at /N/soft/rhel7/trinityrnaseq/2.6.6/Trinity line 1316

Trinity run failed. Must investigate error above. Command is:

Trinity --left /N/dc2/scratch/trinity/database/files/031/dataset_31753.dat --right /N/dc2/scratch/trinity/database/files/031/dataset_31755.dat --seqType fq --max_memory 248G --CPU 8

Beginning attempt 1 of Trinity job at 23/05/18 03:29 Trinity exited with status 2 Finished and found the success command with grep code 1 Beginning attempt 2 of Trinity job at 24/05/18 05:25 Trinity exited with status 1 Finished and found the success command with grep code 1

trinity denovo galaxy • 434 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by tcf.hcdg0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The job is running out of resources during execution.


  • Do some QA on the reads. For this tool, it expects the same reads, in the same order, for the input. The Fastq Interlacer/de-interlaces tools can be used after QA to retain only those paired reads where both survived.
  • Consider using downsampled inputs.
  • Run Trinity on your own Galaxy and supply it with enough resources.

Galaxy tutorials, many of which cover read QA/QC:

Galaxy FAQs:

Galaxy choices: &&

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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