Trinity command for paired sequences (Illumina)

Question

[luigi.marongiu]

Dear all,

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 ()

Thank you

Answer 1

[h.mon]

1. bowtie2 is not bowtie.

2. use --no_version_check to get rid of the

   -ERROR: couldn't run the network check to confirm latest Trinity software version.
   

3. it seem Trinity can't find your fastq files:

   Error, cannot locate file: /path/myFile_1.fq
   

[luigi.marongiu]

Thanks. For 2 and 3, I applied them and now it is going fine; but for 1, since the current version of bowtie is bowtie2, how can I run Trinity with the latest bowtie? Or it is necessary to use bowtie for a de novo assembly?

[h.mon]

I was too terse: bowtie and bowtie2 are two different code bases, and their development is somewhat in parallel. They are not compatible, as the index structure and command line parameters changed a lot. Trinity developers decided to use bowtie, either for convenience (they started with it and didn't want the trouble to change) or because it is more suited than bowtie2 for what they need.