Issue with /root/get-reference-genomes/utils/bed.py

[fredlecerf]

Hello,

I tried to recover and format the version 5 and 6 of the chicken genome. Each time, I get this error (here with GGA6):
Traceback (most recent call last):
File "/root/get-reference-genomes/tools/../utils/collapse-lines-that-share-a-name.py", line 12, in
merged_record.merge(record)
File "/root/get-reference-genomes/utils/bed.py", line 67, in merge
raise Exception('Expected match, but instead: %s != %s' % (self_core, other_core))
Exception: Expected match, but instead: ['chr31', 'CHIR-A2', '1000', '.'] != ['chrUn_NW_020110141v1', 'CHIR-A2', '1000', '.']

I have the same type of error with GGA5:
Traceback (most recent call last):
File "/root/get-reference-genomes/tools/../utils/collapse-lines-that-share-a-name.py", line 12, in
merged_record.merge(record)
File "/root/get-reference-genomes/utils/bed.py", line 67, in merge
raise Exception('Expected match, but instead: %s != %s' % (self_core, other_core))
Exception: Expected match, but instead: ['chr1', 'ALG11', '1000', '.'] != ['chr1_NT_456495v1_random', 'ALG11', '1000', '.']

The commands executed were : ./genome-to-local.sh galGal6 and ./genome-to-local.sh galGal5

Thx