Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

  • #2
    You may want to recreate the indexes on WSL and retry. Is the memory availabe comparable on WSL and linux?

    Comment


    • #3
      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.

      Comment


      • #4
        Originally posted by Jandropu View Post
        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.
        I'm also working with WSL and I was able to use STAR to index and align

        sequences (Ubuntu 16.04, STAR 2.7.0e). I'm not familiar with Ubuntu

        and all my setting are from the biostar handbook. My computer has

        32GB of ram, 4cores (i7) and ssd but uses most of the resource while

        running STAR. Just wanted to reply because this was the only thread that

        I could find about using STAR in WSL when I searched about it.

        Comment


        • #5
          So, STAR works with WSL1 but not WSL2? A related discussion in biostars

          Comment

          Latest Articles

          Collapse

          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
            02-26-2024, 02:07 PM
          • seqadmin
            Multiomics Techniques Advancing Disease Research
            by seqadmin


            New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

            A major leap in the field has
            ...
            02-08-2024, 06:33 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 02-28-2024, 06:12 AM
          0 responses
          21 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-23-2024, 04:11 PM
          0 responses
          70 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          77 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X