This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error during Trinity running with the recent version?

Hi all,

I'm using last version of Trinity (20140717) to make de novo transcriptome assembly of large fastq.gz files, but the program immediately give me the following error

fastool: parsing error, truncated sequence and/or quality detected!
Thread 1 terminated abnormally: Error, cmd: /home/jafarinezhad/software/trinityrnaseq_r20140717/util/..//trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/jafarinezhad/software/trinityrnaseq_r20140717/newreads1.fq.gz >> left.fa died with ret 256 at /home/jafarinezhad/software/trinityrnaseq_r20140717/util/insilico_read_normalization.pl line 719.
CMD finished (0 seconds)
Error, conversion thread failed at /home/jafarinezhad/software/trinityrnaseq_r20140717/util/insilico_read_normalization.pl line 329.
Error, cmd: /home/jafarinezhad/software/trinityrnaseq_r20140717/util/insilico_read_normalization.pl --seqType fq --JM 150G --max_cov 50 --CPU 6 --output /home/jafarinezhad/software/trinityrnaseq_r20140717/trinity_out_dir/insilico_read_normalization --SS_lib_type FR --left /home/jafarinezhad/software/trinityrnaseq_r20140717/newreads1.fq.gz --right /home/jafarinezhad/software/trinityrnaseq_r20140717/newreads2.fq.gz --pairs_together --PARALLEL_STATS  died with ret 7424 at ./Trinity line 1990.

Is anybody faced with this error, how should solve it? Thanks

next-gen assembly rna-seq
• 5,647 views • link
updated by Ram Ram • written by seta seta

Sounds like your fasta files are corrupted, check is something went wrong when you copy your files.

• 0 views • link
written by JC JC

it sounds that they are right during copy. how are they corrupted? any suggested solution?

• 0 views • link
written by seta seta

Even when you didn't get any error message, sometimes bytes just flip and corrupt a compressed file (disk I/O have some errors that cannot be predicted).

• 0 views • link
updated by Ram Ram • written by JC JC

Thank you. But I am again facing an issue. this time it is giving error:

conversion thread failed at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/util/insilico_read_normalization.pl line 333.
Error, cmd: /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/util/insilico_read_normalization.pl --seqType fa --JM 4G  --max_cov 50 --min_cov 1 --CPU 4 --output /home/fuad/Downloads/Trinityoutput/insilico_read_normalization   --max_pct_stdev 10000  --SS_lib_type RF  --left /home/fuad/Downloads/catination/left.fastq --right /home/fuad/Downloads/catination/right.fastq --pairs_together --PARALLEL_STATS   died with ret 7424 at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 2581.
    main::process_cmd("/home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trin"...) called at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 3127
    main::normalize("/home/fuad/Downloads/Trinityoutput/insilico_read_normalization", 50, ARRAY(0x564b84843b70), ARRAY(0x564b84843ba0)) called at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 3074
    main::run_normalization(50, ARRAY(0x564b84843b70), ARRAY(0x564b84843ba0)) called at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/Trinity line 1294

Can anyone please help?

• 0 views • link
updated by Ram Ram • written by fuad.fsu • fuad.fsu

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Trinity analysis error
    written by ongchip • ongchip
    (base) ongchip@ongchip-LINUX:~/ongchip-DP/work/202408$ $TRINITY_HOME/Trinity --seqType fq --max_memory 10G --left A1_1_paired.fq.gz --right A1_2_paired.fq.gz --CPU 2 ______ ____ ____ ____ ____ ______ __ __ | || \ | …
  • Trinity error: conversion thread failed
    written by fuad.fsu • fuad.fsu
    Hie, Can anyone please help me to solve the following error please error: conversion thread failed at /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/util/insilico_read_normalization.pl line 333. Error, cmd: /home/fuad/Downloads/Trinityrnaseq-v2.6.6.wExtSampleData/Trinityrnaseq-v2.6.6/util/insilico_read_normalization.pl --seqType fa …
  • Error, cmd: jellyfish count....util/insilico_read_normalization.pl line 733.
    written by natasha.tilich • natasha.tilich
    ## Heading ##Hello everybody!! I ran the following command (base) [ntilikj@login1 clean_data]$ #!/bin/bash (base) [ntilikj@login1 clean_data]$ #SBATCH -p short #nombre cola (base) [ntilikj@login1 clean_data]$ #SBATCH …
  • Error normalization process Trinity
    written by weimabri • weimabri
    Hello I hope everyone is well. I have a question with this error in the normalization of the data. I use this command ./Trinity --seqType …
  • Failed to create symbolic link. Trinity
    written by mailard • mailard
    **This error appears if my output file is at /mnt/...(drive). But if an output file is in home directory - trinity runs well** And some …
  • Trinity assembly error
    written by MAPK MAPK
    Hi All, I am running this assembly using Trinity feeding the following command: Trinity --seqType fq --max_memory 100G --right file_1.fastq --left file_2.fastq --CPU 16 --output …
  • Issues with running trinity on cluster
    written by dcole • dcole
    Hello, I'm trying to run Trinity Denovo assembler for some RNA-seq analysis. I'm running this on a cluster. It returned the following error to me, …
  • problem with trinity
    written by mra8187 • mra8187
    dear all when i am using Trinity v 2.3.2 by this command .`/Trinity --seqType fq --max_memory 5G --single '/media/mra/4A3B44B64CA65A93/SNP/DATA/Queen-Larvae/SRR1571722/Trimmomatic/SE/SRR1571722-1.trimmed.fastq' --CPU 4` i see error ... …
  • Format convert error while using Trinity Galaxy
    written by utsafar utsafar
    I am using trinity galaxy to assemble [an RNA-Seq dataset][1] from saffron.I imported File1 and File2 directly to trinity galaxy. Now I am trying to …
  • Error during running the first step of Trinity?
    written by seta seta
    Hi friends, I used CLC genomic workbench software for trimming, then the output of this software, which is the trimmed fasta file was exposed to …