I am running Trinity from paired sequences which have been trimmed from low quality and adaptors using Trimmomatic. The output of Trimmomatic is formed by 4 files -- two paired and two unpaired -- and I understand Trinity can get multiple files as comma separated. Here are the commands I wrote:
java -jar /usr/share/java/trimmomatic-0.33.jar PE -threads 16 -phred33 source.1.fq source.2.fq pairedA pairedB unpairedA unpairedB ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:1:true LEADING:5 TRAILING:5 MINLEN:36
Trinity --seqType fq --max_memory 10G --no_bowtie --no_version_check --left pairedA, pairedB --right unpairedA, unpairedB --CPU 10
but i got this error:
Sunday, December 6, 2015: 09:30:45 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/lib/Trinity/util/support_scripts/ExitTester.jar 0 Sunday, December 6, 2015: 09:30:46 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/lib/Trinity/util/support_scripts/ExitTester.jar 1 Error, cannot locate file: at /usr/bin/Trinity line 2150. main::create_full_path(ARRAY(0x1102cf0), 1) called at /usr/bin/Trinity line 1106
which I think is due to the wrong input of for the Trinity command; any tips on how to run this process properly?