About minimap2 result

[Flower9618]

Hi, thank you so much for sharing this useful tool. When I run guppy to do the base modification by using '...modbase.cfg' of guppy and require the .bam out. I guess the alignment information is from minimap2, so I call the .bam outout file minimap2 result. After getting .bam file output, I use pysam, a pacakge in python, to read the file. But there is an error:

[E::bam_read1] CIGAR and query sequence lengths differ for 46bccf77-c5f8-4539-b68a-43aa4145f3aa
Traceback (most recent call last): File "result_addCGInfo.py", line 130, in main(args) File "result_addCGInfo.py", line 64, in main for r in bf: File "pysam/libcalignmentfile.pyx", line 1876, in pysam.libcalignmentfile.AlignmentFile.next
OSError: error -4 while reading file

It seems that there is the conflict between the cigar and the sequence length for read '46bccf77-c5f8-4539-b68a-43aa4145f3aa'. Here is the information about the alignment result of this read: seq.txt

I would like to wonder how this situation happens, thank you very much.