Trinity command can't locate file at line 2173 called at line 1109

1

Entering edit mode

7.9 years ago

IrisChang ▴ 20

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 • 5.4k views

ADD COMMENT • link 7.9 years ago by IrisChang ▴ 20

1

Entering edit mode

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

ADD REPLY • link 7.9 years ago by GenoMax 141k

0

Entering edit mode

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

ADD REPLY • link 7.9 years ago by IrisChang ▴ 20

Login before adding your answer.