Mapped reads not mapping to a real sequence?

Hi,

I’ve been passed down some bam files from RNA-seq that I need to analyze. They were generated with pseudoalignments using Kallisto ( pachterlab.github.io/kallisto/about )
When I run htseq-count one specific bamfile crashes on a specific read:

Error occured when processing input (record #149548485 in file 103805-016-011.kallisto.pseudoalignments.bam):
Expected str, got NoneType   [Exception type: TypeError, raised in _HTSeq.pyx:60]

After delving deeper I realized that the next read (or that specific one if it is 0-based) has some very weird formatting, at least to me:

[149548484]   A00379:576:H7WK3DSX3:4:1101:5421:1016     77    *     0     0     *     *     0     0     GNTCTTTTAAAAAGAGATTAAACCGAAGGTGATTAAAAGACCTTGAAATCCATGACGCAGGGAGAATTGCGTCATTTAAAGCCTAGTTAACGCATTTACTAAACGCAGACGAAAATGGAAAGATTAATTGGGAGTGGTAGGATGAAACAAT     F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
[149548485]   A00379:576:H7WK3DSX3:4:1101:5421:1016     141   *     0     0     *     *     0     0     CTTCCTACTTTTCAGGTTTAAATTTATCTTTTTTCTTCTAAAAGTATGTTTTTATCTTCTAATTTCCCTATCTTCTCTATTCTTTTCTTCGCCTTCCCGTACTTCTGTCTTCCAGTTTTACACTTCAAACTTCTATCTTCTCCAAATTGTT     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF,FFFFFFF,FFFFF:FFF:FF,FFF:FF,F,FFFFF,:FF
[149548486]   A00379:576:H7WK3DSX3:4:1101:13702:1016    67    *     0     0     151M  *     0     0     ANAAATCTAGGCTCCATCAACACTGAATTGCAAGATGTGCAGAGGATCATGGTGGCCAATATTGAAGAAGTGTTACAACGAGGAGAAGCACTCTCAGCATTGGATTCAAAGGCTAACAATTTGTCCAGTCTGTCCAAGAAATACCGCCAGG     F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF     ZW:f:0
[149548487]   A00379:576:H7WK3DSX3:4:1101:13702:1016    131   *     0     0     151M  *     0     0     TATTTTCAGGAAACTGAGCTCACAGAGATGTGTATTAGAATCCAAGTGGAACTTCTGCCTCTAAAGACCTTGCAAGAAAAGAGATGCCCTGAAAATGAAAGGTTGCACCTCATTTAATGAAGCTTAACCCTATGTAGAAAGTCTCTTTCGG     F:FFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF     ZW:f:0
[149548488]   A00379:576:H7WK3DSX3:4:1101:14913:1016    77    *     0     0     *     *     0     0     ANTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTA     F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,::,F::,FF:F:FFFFF,FF:,,::FF:F,F:,,:FFFFFF:F:F::F:FFFFFF,
[149548489]   A00379:576:H7WK3DSX3:4:1101:14913:1016    141   *     0     0     *     *     0     0     GTTTATAGATAGTTGGGTGGTTGGTGTAAATGAGTGAGGCAGGAGTCCGAGGAGGAGGTTAGTTGTGGCAATAAAAATGATTAAGGATACTAGTATAAGAGATCAGGTTCGTCCTTTAGTGTTGTGTATGGTTATCATTTGTTTTGAGGTT     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:F:FFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFF::FFFF:F:FFFFFFFFFFFF::FFF,FFFFFFFFFFFFFFFFFFFF:FFFFFFFF,:F

The read pair at lines 149548486-149548487 are flagged as being mapped, but they aren’t mapped to any known sequence (RNAME is *).

How can I prevent such error?

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