Error during Trinity running with the recent version?
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8.8 years ago
seta ★ 1.8k

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 • 4.7k views
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Sounds like your fasta files are corrupted, check is something went wrong when you copy your files.

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

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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).

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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?

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