Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • STAR error: could not open readFilesIn

    Hi all. I'm quite new to RNA-seq and in particular using the STAR alignment software. I have written a script to map my reads to a reference genome, but it keeps erroring out and giving me this error message:

    EXITING because of fatal input ERROR: could not open readFilesIn=/dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read1.fastq

    Essentially, it cannot seem to open my fastq files, but I cannot figure out why. Here is my script (sorry for the lengthy directory paths)



    module load STAR/2.5.2a


    cd /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017

    mkdir David_data1


    STAR --genomeDir /dfs1/bio/dtatarak/indexes/STAR_Index --readFilesIn /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read1.fastq /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read2.fastq --runThreadN 8 --outFileNamePrefix "David_data1/DT_1"


    Does anyone know what the problem might be? I've scoured the internet, and I can't seem to find a solution.

  • #2
    Are you using a cluster to run this job (likely since you are using modules)? If so check to make sure that "/dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/" is available on the job nodes where the job is actually running.

    Comment


    • #3
      If you are using a cluster or SGE setup, you might try to qlogin and see if you can still find the files and if the paths are correct. You might check if the permissions on those input files are correct for another process accessing them also.

      If you copy and paste the command directly into the command line does it fail the same way or does it work? If it works, that means its probly a cluster submission issue, and if it fails it means you maybe messed up the path to the input file.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Exploring the Dynamics of the Tumor Microenvironment
        by seqadmin




        The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
        07-08-2024, 03:19 PM
      • seqadmin
        Exploring Human Diversity Through Large-Scale Omics
        by seqadmin


        In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
        06-25-2024, 06:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 07-10-2024, 07:30 AM
      0 responses
      26 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-03-2024, 09:45 AM
      0 responses
      201 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-03-2024, 08:54 AM
      0 responses
      212 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-02-2024, 03:00 PM
      0 responses
      193 views
      0 likes
      Last Post seqadmin  
      Working...
      X