Question: Error during Trinity running with the recent version?
0
gravatar for seta
4.0 years ago by
seta1.1k
Sweden
seta1.1k wrote:

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

 

 

rna-seq next-gen assembly • 2.6k views
ADD COMMENTlink written 4.0 years ago by seta1.1k

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

ADD REPLYlink written 4.0 years ago by JC7.8k

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

ADD REPLYlink written 4.0 years ago by seta1.1k

Fastq Quality Read And Score Length Check

 

ADD REPLYlink written 4.0 years ago by rtliu2.0k

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). 

ADD REPLYlink written 4.0 years ago by JC7.8k
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