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yekaizhou / duet

SNP-Assisted SV Calling and Phasing Using ONT
BSD 3-Clause "New" or "Revised" License
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SNP calling not working #10

Open mzwaig opened 1 year ago

mzwaig commented 1 year ago

Hi,

I'm trying to run duet but the SNP calling isn't working.

Thanks, Melissa

[INFO] Check environment variables [INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} by default [INFO] Call variant in contigs: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y [INFO] Chunk number for each contig: 50 49 40 39 37 35 32 30 29 28 28 27 24 22 21 19 17 16 12 13 10 11 32 12 [INFO] 1/7 Call variants using pileup model Calling variants ... Traceback (most recent call last): File "/Project/tools/conda/duet/bin/scripts/../clair3.py", line 94, in main() File "/Project/tools/conda/duet/bin/scripts/../clair3.py", line 88, in main submodule.main() File "/Project/tools/conda/duet/bin/clair3/CallVariantsFromCffi.py", line 347, in main Run(args) File "/Project/tools/conda/duet/bin/clair3/CallVariantsFromCffi.py", line 61, in Run call_variants_from_cffi(args=args, output_config=output_config, output_utilities=output_utilities) File "/Project/tools/conda/duet/bin/clair3/CallVariantsFromCffi.py", line 117, in call_variants_from_cffi tensor, all_position, all_alt_info = CT(args) File "/Project/tools/conda/duet/bin/preprocess/CreateTensorPileupFromCffi.py", line 329, in CreateTensorPileup chunk_result, all_alt_info_list, gvcf_output = pileup_counts_clair3(region, File "/Project/tools/conda/duet/bin/preprocess/CreateTensorPileupFromCffi.py", line 84, in pileup_counts_clair3 chunk_results, all_alt_info_list, gvcf_output = enforce_pileup_chunk_contiguity(results) File "/Project/tools/conda/duet/bin/preprocess/CreateTensorPileupFromCffi.py", line 194, in __enforce_pileup_chunk_contiguity for counts, positions, alt_info_list, gvcf_output in pileups: File "/Project/tools/conda/duet/lib/python3.9/concurrent/futures/_base.py", line 600, in result_iterator yield fs.pop().result() File "/Project/tools/conda/duet/lib/python3.9/concurrent/futures/_base.py", line 440, in result return self.get_result() File "/Project/tools/conda/duet/lib/python3.9/concurrent/futures/_base.py", line 389, in get_result raise self._exception File "/Project/tools/conda/duet/lib/python3.9/concurrent/futures/thread.py", line 52, in run result = self.fn(*self.args, **self.kwargs) File "/Project/tools/conda/duet/bin/preprocess/CreateTensorPileupFromCffi.py", line 63, in _process_region np_counts, positions, alt_info_string_list, gvcf_output = _plp_data_to_numpy( File "/Project/tools/conda/duet/bin/preprocess/CreateTensorPileupFromCffi.py", line 141, in _plp_data_to_numpy size_sizet = np.dtype(np.int).itemsize File "/Project/tools/conda/duet/lib/python3.9/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'int'. np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

yekaizhou commented 1 year ago

Dear Melissa,

Thanks for using Duet. This is because a recent Numpy update has just deprecated np.int. To solve this problem, you can simply replace two "np.int" instances to "int" in /Project/tools/conda/duet/bin/preprocess/CreateTensorPileupFromCffi.py (line 141 and 142).

Please refer to https://github.com/HKU-BAL/Clair3/pull/166/commits/3ea0279d3b53d8d8ab128e6fee3877933f1249ce for your further reference. We will incorporate this to our latest release later.

Thank you, Yekai

jamesdalg commented 1 year ago

@yekaizhou I tried this and modified just the "np.int" instances and changed them to "int". SNPs with clair3 and SV calls with cuteSV work fine, but I still have the following error:

03:41:57 [INFO] ************************* SV CALLING COMPLETED IN 107.985s *************************
03:41:57 [INFO] ************************* SNP PHASING STARTED *************************
mkdir: cannot create directory ‘/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/’: File exists
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr20.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr9.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr1.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr2.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr4.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr5.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr3.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr6.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr7.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr8.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr10.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr11.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr12.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr13.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr14.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr15.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr16.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr17.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr18.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr19.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr21.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chr22.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chrX.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
This is WhatsHap 1.4 running under Python 3.9.0
Traceback (most recent call last):
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1122, in main
    run_whatshap(**vars(args))
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/cli/phase.py", line 363, in run_whatshap
    PhasedVcfWriter(
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 900, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 804, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/ceph/project/davieslab/jdalglei/micromamba/envs/duet/lib/python3.9/site-packages/whatshap/vcf.py", line 704, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4347, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/chrY.vcf'` (mode=`b'r'`) - is it VCF/BCF format?
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr1.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr2.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr3.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr4.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr5.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr6.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr7.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr8.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr9.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr10.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr11.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr12.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr13.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr14.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr15.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr16.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr17.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr18.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr19.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr20.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr21.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr22.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrX.vcf.gz
tbx_index_build failed: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrY.vcf.gz
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr1.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr1.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr1.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrY.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrY.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrY.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr2.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr2.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr2.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr3.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr3.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr3.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr10.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr10.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr10.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr22.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr22.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr22.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr16.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr16.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr16.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr18.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr18.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr18.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr13.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr13.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr13.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr12.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr12.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr12.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr5.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr5.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr5.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr4.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr4.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr4.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr17.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr17.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr17.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr7.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr7.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr7.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr8.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr8.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr8.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr9.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr9.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr9.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr14.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr14.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr14.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr6.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr6.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr6.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr15.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr15.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr15.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr19.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr19.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr19.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr20.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr20.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr20.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr11.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr11.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr11.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr21.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr21.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chr21.vcf.gz'`: No such file or directory
[E::hts_open_format] Failed to open file "/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrX.vcf.gz" : No such file or directory
ERROR: whatshap error: Error while loading variant file /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrX.vcf.gz: [Errno 2] could not open variant file `b'/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//snp_phasing/phased_chrX.vcf.gz'`: No such file or directory
03:42:10 [INFO] ************************* SNP PHASING COMPLETED IN 12.902s *************************
03:42:10 [INFO] ************************* SV PHASING STARTED *************************
03:42:10 [INFO] create output .vcf file
03:42:12 [INFO] extract SNP signatures
03:42:12 [INFO] extract SV signatures
03:42:17 [INFO]   signatures extracted from 1
03:42:18 [INFO]   signatures extracted from 2
03:42:18 [INFO]   signatures extracted from 3
03:42:18 [INFO]   signatures extracted from 4
03:42:18 [INFO]   signatures extracted from 5
03:42:18 [INFO]   signatures extracted from 6
03:42:18 [INFO]   signatures extracted from 7
03:42:18 [INFO]   signatures extracted from 8
03:42:18 [INFO]   signatures extracted from 9
03:42:18 [INFO]   signatures extracted from 10
03:42:19 [INFO]   signatures extracted from 11
03:42:19 [INFO]   signatures extracted from 12
03:42:19 [INFO]   signatures extracted from 13
03:42:19 [INFO]   signatures extracted from 14
03:42:19 [INFO]   signatures extracted from 15
03:42:19 [INFO]   signatures extracted from 16
03:42:19 [INFO]   signatures extracted from 17
03:42:19 [INFO]   signatures extracted from 18
03:42:19 [INFO]   signatures extracted from 19
03:42:19 [INFO]   signatures extracted from 20
03:42:19 [INFO]   signatures extracted from 21
03:42:19 [INFO]   signatures extracted from 22
03:42:19 [INFO]   signatures extracted from X
03:42:19 [INFO]   signatures extracted from Y
03:42:20 [INFO] integrate read weight information
03:42:20 [INFO] calculate read weight statistics
03:42:20 [INFO] predict SV haplotypes in the callset
03:42:20 [INFO] write phased callset into .vcf file
03:42:20 [INFO] ************************* SV PHASING COMPLETED IN 10.264s *************************
03:42:20 [INFO] ************************* DUET FINISHED IN 12571.45s *************************
03:42:20 [INFO] OUTPUT .VCF FILE AT /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute//phased_sv.vcf
cp: cannot stat '/ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/m64176e_230414_121509.hifi_reads_phased_sv.vcf': No such file or directory
[Mon Jun 19 03:42:20 2023]
Error in rule duet:
    jobid: 0
    input: /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.mm2ax_aligned_sorted.bam.bai, /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.mm2ax_aligned_sorted.bam, /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.chm13.mm2ax_aligned_sorted.bam, /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.chm13.mm2ax_aligned_sorted.bam.bai, /ceph/project/davieslab/jdalglei/reference/hg38.fa, /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa
    output: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/m64176e_230414_121509.hifi_reads_duet_cute_hg38.vcf, /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/sniffles/m64176e_230414_121509.hifi_reads_duet_sniffles_hg38.vcf, /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/svim/m64176e_230414_121509.hifi_reads_duet_svim_hg38.vcf, /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/cute/m64176e_230414_121509.hifi_reads_duet_cute_chm13.vcf, /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/sniffles/m64176e_230414_121509.hifi_reads_duet_sniffles_chm13.vcf, /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/svim/m64176e_230414_121509.hifi_reads_duet_svim_chm13.vcf
    shell:

        mkdir -p /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/;
        mkdir -p /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/sniffles/;
        mkdir -p /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/svim/;
        mkdir -p /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/cute/;
        mkdir -p /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/sniffles/;
        mkdir -p /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/svim/;
        duet -t 128 /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.mm2ax_aligned_sorted.bam /ceph/project/davieslab/jdalglei/reference/hg38.fa /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/  -b cutesv;
        cp /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/m64176e_230414_121509.hifi_reads_phased_sv.vcf /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/m64176e_230414_121509.hifi_reads_duet_cute_hg38.vcf;
        duet -t 128 /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.mm2ax_aligned_sorted.bam /ceph/project/davieslab/jdalglei/reference/hg38.fa /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/sniffles/  -b sniffles;
        cp /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/sniffles/m64176e_230414_121509.hifi_reads_phased_sv.vcf /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/sniffles/m64176e_230414_121509.hifi_reads_duet_sniffles_hg38.vcf;
        duet -t 128 /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.mm2ax_aligned_sorted.bam /ceph/project/davieslab/jdalglei/reference/hg38.fa /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/svim/  -b svim;
        cp /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/svim/m64176e_230414_121509.hifi_reads_phased_sv.vcf /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/svim/m64176e_230414_121509.hifi_reads_duet_svim_hg38.vcf;
        duet -t 128 /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.chm13.mm2ax_aligned_sorted.bam /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/cute/  -b cutesv;
        cp  /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/cute/m64176e_230414_121509.hifi_reads_phased_sv.vcf /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/cute/m64176e_230414_121509.hifi_reads_duet_cute_chm13.vcf;
        duet -t 128 /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.chm13.mm2ax_aligned_sorted.bam /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/sniffles/  -b sniffles;
        cp /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/sniffles/m64176e_230414_121509.hifi_reads_phased_sv.vcf /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/sniffles/m64176e_230414_121509.hifi_reads_duet_sniffles_chm13.vcf;
        duet -t 128 /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/bam/m64176e_230414_121509.hifi_reads.chm13.mm2ax_aligned_sorted.bam /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/svim/  -b svim;
        cp /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/svim/m64176e_230414_121509.hifi_reads_phased_sv.vcf /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/chm13/svim/m64176e_230414_121509.hifi_reads_duet_svim_chm13.vcf;

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
jamesdalg commented 1 year ago

To give a bit more insight, it seems as though actually SNP calling happens fine, but it's the SNP phasing where things go wrong.

/project/davieslab/jdalglei/code/sm/logs$ ls /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/sv_calling/ -lrt
total 83864
-rw-r--r-- 1 jdalglei davieslabgrp 85876622 Jun 19 03:41 variants.vcf
/project/davieslab/jdalglei/code/sm/logs$ ls -lrth /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/snp_phasing
total 1.5K
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr1.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr2.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr4.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr3.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr5.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr6.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr8.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr7.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr9.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr10.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr12.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr11.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr13.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr15.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr14.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr17.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr16.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr19.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr18.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr21.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr20.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chrY.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chrX.vcf
-rw-r--r-- 1 jdalglei davieslabgrp    0 Jun 19 03:41 chr22.vcf
-rwxr-xr-x 1 jdalglei davieslabgrp 1.4K Jun 19 03:41 parallel_wh.sh
/project/davieslab/jdalglei/code/sm/logs$ ls -lrth /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/duet/hg38/cute/snp_calling
total 42M
drwxr-sr-x 7 jdalglei davieslabgrp 262M Jun 17 23:33 tmp
drwxr-sr-x 2 jdalglei davieslabgrp 846K Jun 17 23:33 log
-rw-r--r-- 1 jdalglei davieslabgrp  40M Jun 19 03:40 pileup.vcf.gz
-rw-r--r-- 1 jdalglei davieslabgrp 1.5M Jun 19 03:40 pileup.vcf.gz.tbi
-rw-r--r-- 1 jdalglei davieslabgrp  73K Jun 19 03:40 run_clair3.log
yekaizhou commented 1 year ago

Hi @jamesdalg, could you please run "bcftools -h" on the working environment of duet to see if it works?

jamesdalg commented 1 year ago

This fixed the issue. I was able to generate results after this point. @yekaizhou Thanks!

yekaizhou commented 1 year ago

The inconsistency of the numpy library is fixed in our latest release v1.0.