Question: Trinity ERROR during assembling extracted reads
0
gravatar for evodevo110
8 months ago by
evodevo1100
evodevo1100 wrote:

Hello, I am trying to use Trinity due to assemble the reads extracted from fastq files after blast.

$  Trinity --seqType fq --left Forward_top-hits.fastq --right Reverse_top-hits.fastq

This is the error that I have:

Assertion failed: (beg < end), function setBaseRange, file /anaconda/conda-bld/work/trinityrnaseq_r2011-11-26/trinity-plugins/kmer/libseq/merStream.C, line 45.
Error, cmd: /Users/manueldlpro/miniconda3/opt/trinity-date.2011_11_26/trinity-plugins/kmer/meryl/meryl -v -B -m 25 -s both.fa.headless -o meryl_kmer_db -C died with ret 6 at ./Trinity.pl line 626.
trinity assembly • 234 views
ADD COMMENTlink modified 8 months ago by Vijay Lakhujani4.2k • written 8 months ago by evodevo1100
1

I would suggest using a newer version of Trinity. You are using a 2011 version. There has been a lot of new development since then that might fix your issue.

ADD REPLYlink modified 8 months ago • written 8 months ago by Damian Kao15k

Thanks for answering, I installed the last version via anaconda and if I update Trinity it say that I already have the last version.

ADD REPLYlink written 8 months ago by evodevo1100

That's not possible. See the list in the bioconda channel:

You have a really old version installed, you can conda update -n env_name trinity and it should work fine.

ADD REPLYlink modified 8 months ago • written 8 months ago by RamRS22k
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