Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • STAR Aligner quantMode and fatal error

    Hello Everyone,

    I have problems with STAR aligner.
    I want to use the quantMode option in order to have .tab file that I will use for later analysis.

    The first thing I did is the index of the genome:

    Code:
    STAR --runMode genomeGenerate --genomeDir genome/star/ --genomeFastaFiles /genome/Homo_sapiens.GRCh37.75.fa --sjdbGTFfile /genome/Homo_sapiens.GRCh37.75.gtf --runThreadN 20 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS --outFileNamePrefix genome/star/

    from where I obtained this list of files

    Code:
    total 382248
    -rw-rw-r--. 1        617 Mar 26 23:06 chrLength.txt
    -rw-rw-r--. 1       1330 Mar 26 23:06 chrNameLength.txt
    -rw-rw-r--. 1        713 Mar 26 23:06 chrName.txt
    -rw-rw-r--. 1       919 Mar 26 23:06 chrStart.txt
    -rw-rw-r--. 1      22187668 Mar 26 23:22 exonGeTrInfo.tab
    -rw-rw-r--. 1      21831277 Mar 26 23:22 exonInfo.tab
    -rw-rw-r--. 1     784390 Mar 26 23:22 geneInfo.tab
    -rw-rw-r--. 1        346597481 Mar 26 23:22 Log.out
    drwx------. 2         6 Mar 26 23:05 _STARtmp
    -rw-rw-r--. 1        0 Mar 26 23:22 transcriptInfo.tab
    then I run my sample

    Code:
    STAR --genomeDir genome/star --readFilesIn my_fastq/Treated_1_m1.fastq.gz my_fastq/Treated_1_m2.fastq.gz --outSAMtype BAM SortedByCoordinate --sjdbGTFfile genome/Homo_sapiens.GRCh37.75.gtf --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic –alignIntronMax 15000 --outFilterIntronMotifs RemoveNoncanonical --runThreadN 20 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS --outReadsUnmapped fastx --readFilesCommand zcat
    and I have this error,


    Code:
    Mar 27 03:32:36 ..... started STAR run
    Mar 27 03:32:36 ..... loading genome
    
    EXITING because of FATAL ERROR: could not open genome file genome/star2/genomeParameters.txt
    SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions
    
    Mar 27 03:32:36 ...... FATAL ERROR, exiting

    It seems like that he can not find the genomeParameters.txt file but was not even created during the indexing.

    Does anybody had a similar problem or knows the solution?

    Thank you for help
    Last edited by NDUFB11; 03-26-2019, 06:48 PM.

  • #2
    See this: https://github.com/alexdobin/STAR/issues/292

    Use full path for genome dir in your command.

    Comment


    • #3
      Hi GenoMax,

      unfortunately writing the entire path didn't help,

      there must be something in my index structure command line that need to be adjusted I guess.

      the problem is that if I want to use the option

      Code:
      --quantMode TranscriptomeSAM GeneCounts
      I need to use the fasta format along with the GTF format for the index, otherwise I can get the genomeParameters.txt by using only the fasta format
      Thank you for you answer anyways

      Comment


      • #4
        Looks like your genome generation failed. There are missing quite a few files.

        Have a look at
        Log.out
        Are you seeing some errors?
        Usually it should finish with sth. like:
        Mar 13 17:07:06 ..... finished successfully
        DONE: Genome generation, EXITING
        And yes, just to be sure, I'd also use absolute paths as parameters ..

        Comment


        • #5
          Hi sklages,
          I solved the problem by skipping TrascriptomeSAM,
          running just this:

          --quantMode GeneCounts

          Thank you

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM
          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 06:37 PM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          51 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X