Running Star-fusion in parallel

[Gabriel A. C. Gama]

Hello everyone! I would like to know if there is any way of running Star-Fusion in parallel for some samples at the same time

We have a 16 core server with 251gb of RAM, and even if we need a lot of memory per sample, it would still be ok to run 5-6 samples at the same time

I'm a newbie at linux, just starting now, but I got parallel to work with other programs such as cutadapt and I tought I could do the same with STAR-fusion but I'm not sure

[Brian Haas]

Hi Gabriel,

You can try using the script:
   STAR-Fusion/util/STAR-Fusion.run_many_samples.pl

     usage: STAR-Fusion.run_many_samples.pl samples.txt num_parallel [starF options passthru] [--do_remove]

It requires that you have ParaFly installed and in your PATH setting:  https://github.com/ParaFly/ParaFly/releases/tag/v0.1.0

The 'samples.txt' file is just a file containing tab-delimited fields:

sample_name   /path/to/reads_1.fastq    /path/to/reads_2.fastq

It first loads into shared memory the genome index, and will then run up to your num_parallel set number of samples in parallel.  Output directories will be set as the sample name parameter for each.

hth,

~brian

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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Gabriel A. C. Gama]

Thank you very much for the fast response!

After trying many times, I got a problem that I can't seem to solve

Everytime I try to run the many_samples.pl, I get the following error:

"Error, no env var set for CTAT_GENOME_LIB at /home/gabriel.gama/star_fusion/STAR-Fusion-v1.10.0/util/STA

R-Fusion.run_many_samples.pl line 15. "

I tried many things such as 

env CTAT_GENOME_LIB=PATH/ctat_genome_lib_build_dir

env CTAT_GENOME_LIB="PATH/ctat_genome_lib_build_dir"

CTAT_GENOME_LIB=PATH/ctat_genome_lib_build_dir

CTAT_GENOME_LIB="PATH/ctat_genome_lib_build_dir"

And also putting CTAT_GENOME_LIB in my path. 

I'm currently using arch linux in my machine

Any ideas?

[Brian Haas]

Hi Gabriel,

If you're using bash, then you would use the command:

   export CTAT_GENOME_LIB="/the/path/to/your/ctat_genome_lib_build_dir"

let's see if that helps.

best,

~b

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