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Old 07-04-2019, 12:17 AM   #1
Junior Member
Location: Maastricht, The Netherlands

Join Date: Jul 2019
Posts: 2
Unhappy 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/ -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,
Marcha is offline   Reply With Quote

bowtie, index, mapsplice, mapsplice2

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