Hi,

I'm using mirdeep2 for finding miRNAs on mouse data.

I ran mapper.pl as a first step. It runs well and give me output. But throws an error at the end about mapping statistics. Does anyone know what this error is? And I'm not sure if I should rely on my results because of this error.

I ran using the command:

    mapper.pl Sample.fastq -e -h -p ~/refs/mm9 -s Sample.fa -t Sample.arf

And I get this error at the end:

    # reads processed: 24468373
    # reads with at least one reported alignment: 13415055 (54.83%)
    # reads that failed to align: 10102035 (41.29%)
    # reads with alignments suppressed due to -m: 951283 (3.89%)
    Reported 18449906 alignments to 1 output stream(s)
    Mapping statistics
    
    #desc   total   mapped  unmapped        %mapped %unmapped
    Use of uninitialized value $count2 in subtraction (-) at /opt/sam/miRDeep/2.0.5/mapper.pl line 630, <IN> line 18449906.
    Use of uninitialized value $count in subtraction (-) at /opt/sam/miRDeep/2.0.5/mapper.pl line 630, <IN> line 18449906.
    total: Use of uninitialized value $count in print at /opt/sam/miRDeep/2.0.5/mapper.pl line 630, <IN> line 18449906.
            Use of uninitialized value $count2 in print at /opt/sam/miRDeep/2.0.5/mapper.pl line 630, <IN> line 18449906.
            0       Use of uninitialized value $count in division (/) at /opt/sam/miRDeep/2.0.5/mapper.pl line 631, <IN> line 18449906.
    Use of uninitialized value $count2 in division (/) at /opt/sam/miRDeep/2.0.5/mapper.pl line 631, <IN> line 18449906.
    Illegal division by zero at /opt/sam/miRDeep/2.0.5/mapper.pl line 631, <IN> line 18449906.
I was able to solve the issue. I included a new option `-m`, and it started working well.

    mapper.pl sample.fastq -e -h -m -v -p ~/refs/mm9 -s Sample.fa -t Sample.arf

Results:

    parsing fastq to fasta format
    discarding short reads
    collapsing reads
    mapping reads to genome index
    # reads processed: 6409517
    # reads with at least one reported alignment: 4426074 (69.05%)
    # reads that failed to align: 1850959 (28.88%)
    # reads with alignments suppressed due to -m: 132484 (2.07%)
    
    Reported 4984883 alignments to 1 output stream(s)
    trimming unmapped nts in the 3' ends
    Mapping statistics
    #desc   total   mapped  unmapped        %mapped %unmapped
    total: 17205138 9753961 7451177 0.567   0.433
    seq: 17205138   9753961 7451177 0.567   0.433