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Old 07-11-2018, 12:34 AM   #1
Jandropu
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Location: Amsterdam

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Default Running STAR on Windows WSL

WSL can be a great option for those that need to have a Windows OS and cannot access a Linux server.
I have tried to run STAR from Windows WSL with Ubuntu 18 installed. First, I tried the pre-compiled binaries (last release; 2.6), and the program runs, but it does not align anything. I tried with some paired-end data with default options, but after loading the genome, it finishes "successfully" in few seconds and the Aligned.out is empty. Then, I tried compiling from source. After installing dependencies, the program compiled fine although with warnings and it runs, but again it does nothing after loading the genome (but finishes without errors). The Log.out doesn´t help finding the problem:

Code:
Finished loading the genome: Wed Jul 11 09:49:31 2018

Processing splice junctions database sjdbN=230202,   pGe.sjdbOverhang=100
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Created thread # 1
Completed: thread #0
Completed: thread #1
Joined thread # 1
ALL DONE!
Same data and genome index runs fine in a Linux server, and I have just run Hisat2 in WSL successfully with the same fastq files

I wonder if someone managed to run STAR on WSL. I would appreciate your feedback (and Alex's one if he sees this thread)

Thanks
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Old 07-11-2018, 01:07 AM   #2
GenoMax
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You may want to recreate the indexes on WSL and retry. Is the memory availabe comparable on WSL and linux?
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Old 07-15-2018, 11:37 PM   #3
Jandropu
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Quote:
Originally Posted by GenoMax View Post
You may want to recreate the indexes on WSL and retry. Is the memory availabe comparable on WSL and linux?
Both are i5 with 16gb. I tried your suggestion, but I have just stopped index generation after 4 days running.

I guess I will stick to Hisat2 and/or Salmon. Both run really fast in this machine using WSL.
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