Question: Trinity command can't locate file at line 2173 called at line 1109
0
gravatar for IrisChang
2.8 years ago by
IrisChang0
IrisChang0 wrote:

Hi,

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/runMe.sh and it ran success. How do I fix this error?

Thanks for any suggestion

assembly • 1.8k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by IrisChang0
1

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

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax65k

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

ADD REPLYlink written 2.8 years ago by IrisChang0
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