Trinity assembly from Trimmomatic output

Question

[luigi.marongiu]

Hello,

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

followed by

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?

Thank you

Answer 1

[h.mon]

1. Trinity can run Trimmomatic for you with --trimmomatic
2. The cause for your error is you have a space between file names on the Trinity call.
3. If if you fix the space, your Trinity command still will be wrong, you can not pair pairedA.fq with unpairedA.fq - this is what you are doing with your --left and --right parameters

[luigi.marongiu]

I knew about (1), but then how can I use the parameters to run it? and I had the trimmed data already. For (2) it worked, but then I got a memory error message; for (3) how shall I feed the files to Trinity? -- left pairedA,pairedB --right unpairedA,unpairedB? Or simply --left pairedA --right pairedB?

[h.mon]

Assuming A and B refers to read 1 and read 2, then yes, either --left pairedA --right pairedB, or read Trinity FAQ.