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  • Error when bbmapping RNA-seq data

    Hello

    I was using BBMap already for successful mapping of RNA-seq data (paired-end, Illumina) to a multi-FASTA transcriptome. Now I tried to map the very same data to the human GRCh38 genome (downloaded from NCBI human genome resources). I used the following command:
    bbmap.sh ref=$mapping_ref build="$BBmap_ref_ID" in=$BBduked_reads1 in2=$BBduked_reads2 \
    outu=unmapped_"$name1"_"$date".sam outm=mapped_"$name1"_"$date".sam \
    maxindel=200k mdtag=true sam=1.4 subfilter=3 pairedonly=true
    Unfortunately, I got the following error:
    [...]
    Retaining first best site only for ambiguous mappings.
    Writing reference.
    Executing dna.FastaToChromArrays2 [/scratch/hpc-prf-ptma2/ptma2001/bbmap/GRCh38_genome_16032022.fna, 6, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]

    Set genScaffoldInfo=true
    Writing chunk 1
    Writing chunk 2
    Exception in thread "main" java.lang.NumberFormatException: For input string: "ӌ�jHN�H��¬���l��,ΚK��/S��ͩm���T
    �!�l��X��o�ã’*s$�s^��m�h
    J@�
    �m��$֧����@�H,���xI%_ Uz�?� S�B�2[*i�_����)i�NEր�ٜ�?Z�i£�� "
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:580)
    at java.lang.Integer.parseInt(Integer.java:615)
    at dna.Data.setGenome2(Data.java:1016)
    at dna.Data.setGenome(Data.java:769)
    at align2.BBMap.loadIndex(BBMap.java:316)
    at align2.BBMap.main(BBMap.java:32)

    Would you have any idea, why this error comes up and how I could solve it?

    Thanks a lot in advance and have a great day,

    Elena

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