I ran Trinity to create a de novo alignment of two paired files <myFile_1.fq> and <myFile_2.fq>, with the following:
Trinity --seqType fq --max_memory 10G --no_bowtie --left /path/myFile_1.fq --right /path/myFile_2.fq --CPU 10
but i got the error:
$ Trinity version: v2.1.1 -ERROR: couldn't run the network check to confirm latest Trinity software version. Saturday, December 5, 2015: 14:49:24 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/lib/Trinity/util/support_scripts/ExitTester.jar 0 Saturday, December 5, 2015: 14:49:25 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/lib/Trinity/util/support_scripts/ExitTester.jar 1 Error, cannot locate file: /path/myFile_1.fq at /usr/bin/Trinity line 2150. main::create_full_path(ARRAY(0x25e9eb8), 1) called at /usr/bin/Trinity line 1106
What I got wrong?
In addition, I had to remove Bowtie -- although the Bowtie2 command is also present in the folder /usr/bin/ of Linux and I can run Bowtie2 from a terminal opened in any location. -- otherwise I get the error:
$ Error, cannot find path to bowtie () or bowtie-build ()