Key error in hsr step

[aysegokce]

Hello,
I am running coral. When I'm running the hsr function, it throws the following error.

Performing HSR mode with options:
mode: hsr
lr_bam: haplotagged_bam/haplotagged.bam
cycles: coral/_amplicon1_cycles.txt
cn_seg: coral/haplotagged.cns
output_prefix: coral/amplicon1_cycle_hsr
normal_cov: 20.8
bp_match_cutoff: 100
bp_match_cutoff_clustering: 2000

Creating bed-converted cycles file: coral/amplicon1_cycle_hsr_converted_cycles.bed
ecDNA intervals:
['chr1', 247363104, 247363325]
['chr1', 246191675, 246818013]
['chr1', 246819348, 247687160]
['chr1', 247693213, 247941526]
['chr1', 150511311, 150611311]
['chr1', 246317043, 246818013]
['chr1', 246819348, 247687160]
['chr1', 247693213, 247941526]
Fetched 194670 chimeric alignments.
Traceback (most recent call last):
  File "/data/KolmogorovLab/keskusa2/tools/CoRAL/src/CoRAL.py", line 164, in <module>
    hsr_mode(args)
  File "/data/KolmogorovLab/keskusa2/tools/CoRAL/src/CoRAL.py", line 38, in hsr_mode
    hsr.locate_hsrs(args)
  File "/vf/users/KolmogorovLab/keskusa2/tools/CoRAL/src/hsr.py", line 134, in locate_hsrs
    bp_list.append(interval2bp(rr_int[ri], rr_int[ri + 1], (r, ri, ri + 1), int(r_int[ri + 1][0]) - int(r_int[ri][1])) + [q_[ri], q_[ri + 1]])
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/vf/users/KolmogorovLab/keskusa2/tools/CoRAL/src/breakpoint_utilities.py", line 293, in interval2bp
    if (global_names.chr_idx[R2[0]] < global_names.chr_idx[R1[0]]) or (global_names.chr_idx[R2[0]] == global_names.chr_idx[R1[0]] and R2[1] < R1[2]):
        ~~~~~~~~~~~~~~~~~~~~^^^^^^^
KeyError: 'chrUn_KI270337v1'

This is how I am running it:

CoRAL.py hsr --lr_bam haplotagged_bam/haplotagged.bam --cycles coral/_amplicon1_cycles.txt --cn_seg coral/haplotagged.cns --normal_cov 20.8 --output_prefix coral/amplicon1_cycle_hsr

Best
Ayse

[maxanes]

Hi, I am getting the same error?