hardingnj
commented
2 years ago Seems to be the same issue as described here: https://github.com/cggh/scikit-allel/issues/376
Workaround: https://github.com/cggh/scikit-allel/issues/376#issuecomment-1132116452
I am getting an error when I run a new xpclr command, it shows that
Traceback (most recent call last): File "/opt/miniconda3/bin/xpclr", line 4, in
import('pkg_resources').run_script('xpclr==1.1.2', 'xpclr')
File "/opt/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/opt/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/opt/miniconda3/lib/python3.7/site-packages/xpclr-1.1.2-py3.7.egg/EGG-INFO/scripts/xpclr", line 196, in
File "/opt/miniconda3/lib/python3.7/site-packages/xpclr-1.1.2-py3.7.egg/EGG-INFO/scripts/xpclr", line 102, in main
File "/opt/miniconda3/lib/python3.7/site-packages/xpclr-1.1.2-py3.7.egg/xpclr/util.py", line 133, in load_vcf_format_data
File "/opt/miniconda3/lib/python3.7/site-packages/xpclr-1.1.2-py3.7.egg/xpclr/util.py", line 117, in load_vcf_wrapper
File "/home/hoo/.local/lib/python3.7/site-packages/allel/io/vcf_read.py", line 308, in read_vcf
samples=samples, transformers=transformers
File "/home/hoo/.local/lib/python3.7/site-packages/allel/io/vcf_read.py", line 1138, in iter_vcf_chunks
fields, samples, headers, it = _iter_vcf_stream(stream, kwds)
File "/home/hoo/.local/lib/python3.7/site-packages/allel/io/vcf_read.py", line 1636, in _iter_vcf_stream
headers = _read_vcf_headers(stream)
File "/home/hoo/.local/lib/python3.7/site-packages/allel/io/vcf_read.py", line 1763, in _read_vcf_headers
raise RuntimeError('VCF file is missing mandatory header line ("#CHROM...")')
RuntimeError: VCF file is missing mandatory header line ("#CHROM...")**
but the vcf file is well formated.