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NKI-CCB / imfusion

Tool for identifying transposon insertions and their effects from RNA-seq data.
MIT License
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Add option to set STAR memory limit #2

Open mschubert opened 6 years ago

mschubert commented 6 years ago

Hi,

I've been trying out this package, I think it's a very nice idea!

I've run into the following issue: by default, STAR limits the memory size to 30 GB. If it passes that treshold, it exists with the message:

Apr 01 14:43:41 ..... Started STAR run
Apr 01 14:43:41 ... Starting to generate Genome files

EXITING because of FATAL ERROR: limitGenomeGenerateRAM=31000000000 is too small for your genome
SOLUTION: specify limitGenomeGenerateRAM not less than 35000000000 and make RAM available

However, if I run imfusion with --limitGenomeGenerateRAM, this option causes an error in the Python parser and is not passed on to STAR.

As a workaround, I added this option to /usr/lib64/python3.5/site-packages/imfusion/external/star.py:

--- star.py.backup      2018-05-10 12:04:31.000000000 -0000
+++ star.py     2018-05-09 13:51:38.000000000 -0000
@@ -33,7 +33,8 @@ def star_index(fasta_path,
     args = [
         'STAR', '--runMode', 'genomeGenerate', '--genomeDir', str(output_dir),
         '--genomeFastaFiles', str(fasta_path), '--sjdbGTFfile', str(gtf_path),
-        '--sjdbOverhang', str(overhang), '--runThreadN', str(threads)
+        '--sjdbOverhang', str(overhang), '--runThreadN', str(threads),
+        '--limitGenomeGenerateRAM', '50000000000'
     ]

     run_command(args=args, log_path=log_path)

It would be nice if imfusion would pass additional command-line parameters to STAR or tophat on the command-line instead.

jrderuiter commented 6 years ago

Thanks for the tip, I'll have a look at including the extra parameter!