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sstadick / perbase

Per-base per-nucleotide depth analysis
MIT License
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'Chromosome not found in BAM/CRAM header' #50

Closed Surar closed 2 years ago

Surar commented 2 years ago

Hi, thanks for helping me with my previous Issue. I got an error message as below

thread '' panicked at 'Chromosome not found in BAM/CRAM header', /opt/conda/conda-bld/perbase_1645626738058/work/src/lib/par_granges.rs:289:18 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

however, there are chromosomes information in my file (I have attached the first page of it). so not sure what is the problem. many thanks, Surar

Screenshot 2022-04-28 at 13 52 43
Surar commented 2 years ago

the problem was in the bed file used with the option perbase base-depth -b.

many thanks

paulahsan commented 4 months ago

If anybody encountered this problem: I get rid of all the chromosome scaffolds/contigs and kept the regular chromosomes, 1:23, X,Y,M and error was gone.