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Roberts Lab Documents
http://sr320.github.io/LabDocs/
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Trinity error on Emu #672

Closed sr320 closed 6 years ago

sr320 commented 6 years ago

Error, cannot locate file: at /home/shared/trinityrnaseq-Trinity-v2.4.0/Trinity line 2429

suggestions welcome I going to guess maybe something to do with PATH?

srlab@emu:~/sr320$ Trinity \
> --seqType fq \
> --left data/NR021_S8_L001_R1_001.fastq, data/NR021_S8_L002_R1_001.fastq \
> --right data/NR021_S8_L001_R2_001.fastq, data/NR021_S8_L002_R2_001.fastq \
> CPU 24 --trimmomatic --max_memory 48G
Left read files: $VAR1 = [
          'data/NR021_S8_L001_R1_001.fastq',
          '',
          'data/NR021_S8_L002_R1_001.fastq'
        ];
Right read files: $VAR1 = [
          'data/NR021_S8_L001_R2_001.fastq',
          '',
          'data/NR021_S8_L002_R2_001.fastq',
          'CPU',
          '24'
        ];
Trinity version: Trinity-v2.4.0
-currently using the latest production release of Trinity.

Friday, August 4, 2017: 11:17:43    CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/shared/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 0
Friday, August 4, 2017: 11:17:43    CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/shared/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/ExitTester.jar 1
Error, cannot locate file:  at /home/shared/trinityrnaseq-Trinity-v2.4.0/Trinity line 2429.
    main::create_full_path(ARRAY(0x1abee80), 1) called at /home/shared/trinityrnaseq-Trinity-v2.4.0/Trinity line 1159
sr320 commented 6 years ago

RESOLVED NO SPACE between files.

this works..

 Trinity \
--seqType fq \
--left data/NR021_S8_L001_R1_001.fastq,data/NR021_S8_L002_R1_001.fastq \
--right data/NR021_S8_L001_R2_001.fastq,data/NR021_S8_L002_R2_001.fastq \
--CPU 24 --trimmomatic --max_memory 48G