Thank you for developing this software, it is very helpful to me.
But I encountered a problem while using it. It seems that there is a problem with my file format. But based on looking at your source code, I found that this file was generated by grmpy. This confused me. After checking your source code, I still can't found problem. The following is my error message:
[E::idx_find_and_load] Could not retrieve index file for 'paragraph_inv/variants.vcf.gz'
2023-08-30 20:36:48,691 ERROR Traceback (most recent call last):
2023-08-30 20:36:48,691 ERROR File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 161, in update_vcf_from_grmpy record = header.new_record(contig=raw_record.chrom, start=raw_record.start, stop=raw_record.stop, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-08-30 20:36:48,692 ERROR File "pysam/libcbcf.pyx", line 2101, in pysam.libcbcf.VariantHeader.new_record
2023-08-30 20:36:48,692 ERROR File "pysam/libcbcf.pyx", line 3247, in pysam.libcbcf.VariantRecord.alleles.set
2023-08-30 20:36:48,692 ERROR ValueError: must set at least 2 alleles
2023-08-30 20:36:48,692 ERROR During handling of the above exception, another exception occurred:
2023-08-30 20:36:48,692 ERROR Traceback (most recent call last):
2023-08-30 20:36:48,699 ERROR File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 340, in run vcfupdate.update_vcf_from_grmpy(vcf_input_path, grmpyOutput, result_vcf_path, sample_names)
2023-08-30 20:36:48,699 ERROR File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 164, in update_vcf_from_grmpy raise Exception("Format error in vcf line: " + str(raw_record))
2023-08-30 20:36:48,700 ERROR Exception: Format error in vcf line: chr1 4203 syri.INV.551237 . . . PASS SVLEN=2949;SVTYPE=INV;END=7152;GRMPY_ID=test_sort.vcf.gz@5b86c07c81908a94739dfe790e732ecf07909ff3fc7a02e1113cde7f9653acc5:1
Traceback (most recent call last):
File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 161, in update_vcf_from_grmpy
record = header.new_record(contig=raw_record.chrom, start=raw_record.start, stop=raw_record.stop,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pysam/libcbcf.pyx", line 2101, in pysam.libcbcf.VariantHeader.new_record
File "pysam/libcbcf.pyx", line 3247, in pysam.libcbcf.VariantRecord.alleles.set
ValueError: must set at least 2 alleles
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 353, in
main()
File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 349, in main
run(args)
File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 340, in run
vcfupdate.update_vcf_from_grmpy(vcf_input_path, grmpyOutput, result_vcf_path, sample_names)
File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 164, in update_vcf_from_grmpy
raise Exception("Format error in vcf line: " + str(raw_record))
Exception: Format error in vcf line: chr1 4203 syri.INV.551237 . . . PASS SVLEN=2949;SVTYPE=INV;END=7152;GRMPY_ID=test_sort.vcf.gz@5b86c07c81908a94739dfe790e732ecf07909ff3fc7a02e1113cde7f9653acc5:1
Thank you for developing this software, it is very helpful to me.
But I encountered a problem while using it. It seems that there is a problem with my file format. But based on looking at your source code, I found that this file was generated by grmpy. This confused me. After checking your source code, I still can't found problem. The following is my error message:
[E::idx_find_and_load] Could not retrieve index file for 'paragraph_inv/variants.vcf.gz'
2023-08-30 20:36:48,691 ERROR Traceback (most recent call last):
2023-08-30 20:36:48,691 ERROR File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 161, in update_vcf_from_grmpy record = header.new_record(contig=raw_record.chrom, start=raw_record.start, stop=raw_record.stop, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-08-30 20:36:48,692 ERROR File "pysam/libcbcf.pyx", line 2101, in pysam.libcbcf.VariantHeader.new_record
2023-08-30 20:36:48,692 ERROR File "pysam/libcbcf.pyx", line 3247, in pysam.libcbcf.VariantRecord.alleles.set
2023-08-30 20:36:48,692 ERROR ValueError: must set at least 2 alleles
2023-08-30 20:36:48,692 ERROR During handling of the above exception, another exception occurred:
2023-08-30 20:36:48,692 ERROR Traceback (most recent call last):
2023-08-30 20:36:48,699 ERROR File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 340, in run vcfupdate.update_vcf_from_grmpy(vcf_input_path, grmpyOutput, result_vcf_path, sample_names)
2023-08-30 20:36:48,699 ERROR File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 164, in update_vcf_from_grmpy raise Exception("Format error in vcf line: " + str(raw_record))
2023-08-30 20:36:48,700 ERROR Exception: Format error in vcf line: chr1 4203 syri.INV.551237 . . . PASS SVLEN=2949;SVTYPE=INV;END=7152;GRMPY_ID=test_sort.vcf.gz@5b86c07c81908a94739dfe790e732ecf07909ff3fc7a02e1113cde7f9653acc5:1
Traceback (most recent call last):
File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 161, in update_vcf_from_grmpy
record = header.new_record(contig=raw_record.chrom, start=raw_record.start, stop=raw_record.stop,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pysam/libcbcf.pyx", line 2101, in pysam.libcbcf.VariantHeader.new_record
File "pysam/libcbcf.pyx", line 3247, in pysam.libcbcf.VariantRecord.alleles.set
ValueError: must set at least 2 alleles
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 353, in
main()
File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 349, in main
run(args)
File "/public2/wangyz/bin/paragraph-v2.4a-binary/bin/multigrmpy.py", line 340, in run
vcfupdate.update_vcf_from_grmpy(vcf_input_path, grmpyOutput, result_vcf_path, sample_names)
File "/public2/wangyz/bin/paragraph-v2.4a-binary/lib/python3/grm/vcfgraph/vcfupdate.py", line 164, in update_vcf_from_grmpy
raise Exception("Format error in vcf line: " + str(raw_record))
Exception: Format error in vcf line: chr1 4203 syri.INV.551237 . . . PASS SVLEN=2949;SVTYPE=INV;END=7152;GRMPY_ID=test_sort.vcf.gz@5b86c07c81908a94739dfe790e732ecf07909ff3fc7a02e1113cde7f9653acc5:1