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MapSplice2 does not recognize my Bowtie indexes



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  • MapSplice2 does not recognize my Bowtie indexes

    Hi everybody,

    I wannted to start working with MapSplice2, however, I run into the problem that it does not recognize my Bowtie1 indexes (build using v1.1.1).

    I am using this command:
    python ${PROGRAMDIR}MapSplice-v2.2.1/mapsplice.py -c ${GENOMEDIR}MapSplice -x ${GENOMEDIR}MapSplice/bt1_GRCh38_apr2019 -1 ${READ1}${SUFFIX2} -2 ${READ2}${SUFFIX2} --threads 6 --output ${align_DIR_MapSplice}${READ1:${#SOURCEDIR}:-${#SUFFIX1}-${#PAIR1}}MapSplice.sam

    This code makes mapsplice2 run:
    [Thu Jul 4 06:32:24 2019] Beginning Mapsplice run (MapSplice v2.2.1)
    [Thu Jul 4 06:32:24 2019] Bin directory: /share/tools/MapSplice-v2.2.1/bin/
    [Thu Jul 4 06:32:24 2019] Preparing output location /share/analysis/CEFIC/CEFIC_testdata/HeCaToS_APA/Trimmed_reads_trimmomatic/MapSplice2/APA_MapSplice.sam/
    [Thu Jul 4 06:32:24 2019] Checking files or directory: /share/analysis/CEFIC/CEFIC_testdata/HeCaToS_APA/Trimmed_reads_trimmomatic/APA_The_000_2_R1.fastq
    [Thu Jul 4 06:32:24 2019] Checking files or directory: /share/analysis/CEFIC/CEFIC_testdata/HeCaToS_APA/Trimmed_reads_trimmomatic/APA_The_000_2_R2.fastq
    [Thu Jul 4 06:32:24 2019] Checking files or directory: /share/tools/data/genomes/GRCh38_r96_april2019/MapSplice/
    [Thu Jul 4 06:32:24 2019] Checking Bowtie index files
    [Thu Jul 4 06:32:24 2019] Building Bowtie index for reference sequence

    But it can not find my bowtie1 indexes and tries to build them. Strangely, it actually starts overwriting the indexes I have already created. After about 6 hours, building the indexes fails, returning this error:
    Error: Building Bowtie index files failed /share/tools/data/genomes/GRCh38_r96_april2019//MapSplice/bt1_GRCh38_apr2019.*

    What is wrong with my code?
    How do I get MapSplice to recognize the indezes I build myself?

    Thank you already,

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