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MapSplice2 gives error if the thread count (-p value) is greater than 2

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  • MapSplice2 gives error if the thread count (-p value) is greater than 2

    Hello! I get a multi-threading error while using MapSplice2. All the reference fasta files and index files were generated accordingly, as mentioned in the website. (http://www.netlab.uky.edu/p/bioinfo/MapSplice2UserGuide)

    I get an error after it evaluates given files/parameters but before starting Mapsplice-multithread when the thread count was -p55. Then I made it run by default which is -p 1. It was working. It also works for -p 2. More than 2 it does not work

    But I want to run it on more number of threads for parallel aligning as it's taking so much time for default setting. Please help me out with this.


    python2 software/MapSplice2/mapsplice.py -1 reads/file_1_trim.fastq -2 reads/file_2_trim.fastq --fusion -c mapsplice_fasta_files/ -x index_files/index -p 55 -o masplice_out

    -----------------------------------------------
    [Thu Jul 22 17:53:58 2021] Beginning Mapsplice run (MapSplice v2.2.1)
    [Thu Jul 22 17:53:58 2021] Bin directory: software/MapSplice2/bin/
    [Thu Jul 22 17:53:58 2021] Preparing output location masplice_out/
    [Thu Jul 22 17:53:58 2021] Checking files or directory: reads/file_1_trim.fastq
    [Thu Jul 22 17:53:58 2021] Checking files or directory: reads/file_2_trim.fastq
    [Thu Jul 22 17:53:58 2021] Checking files or directory: mapsplice_fasta_files//
    [Thu Jul 22 17:53:58 2021] Checking Bowtie index files
    [Thu Jul 22 17:53:58 2021] Inspecting Bowtie index files
    [Thu Jul 22 17:53:58 2021] Checking reference sequence length
    [Thu Jul 22 17:53:58 2021] Checking consistency of Bowtie index and reference sequence
    [Thu Jul 22 17:53:58 2021] Checking read format
    -----[Read Format: FASTQ]
    -----[Read Type: Pair End]
    -----[Total # Reads: 31643736]
    -----[Max Read Length: 101]
    -----[Min Read Length: 31]
    -----[Max Quality Score: 74]
    -----[Min Quality Score: 35]
    -----[Quality Score Scale: Phred+33]
    [Thu Jul 22 17:54:14 2021] Running MapSplice multi-thread
    [MapSplice Running Failed]
    Error: Running MapSplice multi-thread failed: -11
    Last edited by mali_s; 07-29-2021, 12:34 AM.
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