Question: Trinity command can't locate file at line 2173 called at line 1109
gravatar for IrisChang
3.3 years ago by
IrisChang0 wrote:


I have had successfully run Trinity for de novo assembly on my server, but recently ran in to this error:

Error, cannot locate file: heat_R1_P.fastq.gz at /home/program/trinityrnaseq-2.2.0/Trinity line 2173.
main::create_full_path('ARRAY(0x282ac10)', 1) called at /home/program/trinityrnaseq-2.2.0/Trinity line 1109

my command line is:

Trinity --seqType fq --max_memory 10G --left ctl_R1_P.fastq.gz,heat_R1_P.fastq.gz --right ctl_R2_P.fastq.gz,heat_R2_P.fastq.gz --bypass_java_version_check --CPU 6 --no_version_check

Trinity version: v2.1.1

I have test /home/program/trinityrnaseq-2.2.0/sample_data/test_Trinity_Assembly/ and it ran success. How do I fix this error?

Thanks for any suggestion

assembly • 2.1k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by IrisChang0

Error is clear. The file does not seem to be available in the directory that you are running your command from.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax73k

I just check the path of my input file and It works, thanks. ; )

ADD REPLYlink written 3.3 years ago by IrisChang0
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