TRINITY ERROR

[Jyoti Sharma]

Hey all,

I am currently using trinity with the same parameters i used previously with my old samples but now i am getting this error. can anyone help? please.

 Trinity --seqType fq --max_memory 20G --left GSER_removed_R1.fastq,GSFR_removed_R1.fastq,GSGR_removed_R1.fastq,GSHR_removed_R1.fastq --right GSER_removed_R2.fastq,GSFR_removed_R2.fastq,GSGR_removed_R2.fastq,GSHR_removed_R2.fastq --CPU 2 --output Roottrinity_out_dir


     ______  ____   ____  ____   ____  ______  __ __
    |      ||    \ |    ||    \ |    ||      ||  |  |
    |      ||  D  ) |  | |  _  | |  | |      ||  |  |
    |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
      |  |  |    \  |  | |  |  | |  |   |  |  |___, |
      |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
      |__|  |__|\_||____||__|__||____|  |__|  |____/


Left read files: $VAR1 = [
          'GSER_removed_R1.fastq',
          'GSFR_removed_R1.fastq',
          'GSGR_removed_R1.fastq',
          'GSHR_removed_R1.fastq'
        ];
Right read files: $VAR1 = [
          'GSER_removed_R2.fastq',
          'GSFR_removed_R2.fastq',
          'GSGR_removed_R2.fastq',
          'GSHR_removed_R2.fastq'
        ];
Monday, May 6, 2024: 19:39:28 CMD: mkdir -p /media/user/Expansion/NGS/trinityrnaseq-master/Roottrinity_out_dir
Monday, May 6, 2024: 19:39:28 CMD: mkdir -p /media/user/Expansion/NGS/trinityrnaseq-master/Roottrinity_out_dir/chrysalis


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 50 Coverage --
---------------------------------------------------------------

# running normalization on reads: $VAR1 = [
          [
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R1.fastq',
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSFR_removed_R1.fastq',
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSGR_removed_R1.fastq',
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSHR_removed_R1.fastq'
          ],
          [
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R2.fastq',
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSFR_removed_R2.fastq',
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSGR_removed_R2.fastq',
            '/media/user/Expansion/NGS/trinityrnaseq-master/GSHR_removed_R2.fastq'
          ]
        ];


Monday, May 6, 2024: 19:39:28 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 20G  --max_cov 50 --min_cov 1 --CPU 2 --output /media/user/Expansion/NGS/trinityrnaseq-master/Roottrinity_out_dir/insilico_read_normalization   --max_pct_stdev 10000  --left /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R1.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSFR_removed_R1.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSGR_removed_R1.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSHR_removed_R1.fastq --right /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R2.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSFR_removed_R2.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSGR_removed_R2.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSHR_removed_R2.fastq --pairs_together --PARALLEL_STATS  
Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R1.fastq >> left.fa
CMD: seqtk-trinity seq -A /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R2.fastq >> right.fa
Error, not recognizing read name formatting: [A01686:57:H7MHHDSXC:3:1101:1000:9455]

If your data come from SRA, be sure to dump the fastq file like so:

SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra

Thread 1 terminated abnormally: Error, cmd: seqtk-trinity seq -A /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R1.fastq >> left.fa died with ret 512 at /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl line 762.
Error, not recognizing read name formatting: [A01686:57:H7MHHDSXC:3:1101:1000:9455]

If your data come from SRA, be sure to dump the fastq file like so:

SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra

Thread 2 terminated abnormally: Error, cmd: seqtk-trinity seq -A /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R2.fastq >> right.fa died with ret 512 at /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl line 762.
Error, conversion thread failed at /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl line 333.
Error, cmd: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 20G  --max_cov 50 --min_cov 1 --CPU 2 --output /media/user/Expansion/NGS/trinityrnaseq-master/Roottrinity_out_dir/insilico_read_normalization   --max_pct_stdev 10000  --left /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R1.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSFR_removed_R1.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSGR_removed_R1.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSHR_removed_R1.fastq --right /media/user/Expansion/NGS/trinityrnaseq-master/GSER_removed_R2.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSFR_removed_R2.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSGR_removed_R2.fastq,/media/user/Expansion/NGS/trinityrnaseq-master/GSHR_removed_R2.fastq --pairs_together --PARALLEL_STATS   died with ret 7424 at /usr/lib/trinityrnaseq/Trinity line 2589.
main::process_cmd("/usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --"...) called at /usr/lib/trinityrnaseq/Trinity line 3109
main::normalize("/media/user/Expansion/NGS/trinityrnaseq-master/Roottrinity_ou"..., 50, ARRAY(0x556a1f018e20), ARRAY(0x556a1efcdb60)) called at /usr/lib/trinityrnaseq/Trinity line 3056
main::run_normalization(50, ARRAY(0x556a1f018e20), ARRAY(0x556a1efcdb60)) called at /usr/lib/trinityrnaseq/Trinity line 1302