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

    Hello! I am using MapSplice2 to generate fusion candidates for Arabidopsis thaliana RNA-Seq data. 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 if the p value is 2. Greater 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.

    HTML Code:
    [sklab202@localhost ERR1876170]$ python2 /mnt/storage/sklab202/software/MapSplice2/mapsplice.py -1 reads/ERR1876170_1_trim.fastq -2 reads/ERR1876170_2_trim.fastq --fusion -c /mnt/storage/sklab202/genome_files/mapsplice_fasta_files/ -x /mnt/storage/sklab202/geno[sklab202@localhost ERR1876170]$ python2 /mnt/storage/sklab202/software/MapSplice2/mapsplice.py -1 reads/ERR1876170_1_trim.fastq -2 reads/ERR1876170_2_trim.fastq --fusion -c /mnt/storage/sklab202/genome_files/mapsplice_fasta_files/ -x /mnt/storage/sklab202/genome_files/index_files_mapsplice/at_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: /mnt/storage/sklab202/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/ERR1876170_1_trim.fastq
    [Thu Jul 22 17:53:58 2021] Checking files or directory: reads/ERR1876170_2_trim.fastq
    [Thu Jul 22 17:53:58 2021] Checking files or directory: /mnt/storage/sklab202/genome_files/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:  -11me_files/index_files_mapsplice/at_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: /mnt/storage/sklab202/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/ERR1876170_1_trim.fastq
    [Thu Jul 22 17:53:58 2021] Checking files or directory: reads/ERR1876170_2_trim.fastq
    [Thu Jul 22 17:53:58 2021] Checking files or directory: /mnt/storage/sklab202/genome_files/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
    Also, it does work for another plant species. I get this error only for this species

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