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bcf tools error and error in whatshap #29

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kprabhu-soundag opened this issue Sep 1, 2022 · 4 comments
Open

bcf tools error and error in whatshap #29

kprabhu-soundag opened this issue Sep 1, 2022 · 4 comments

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@kprabhu-soundag
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Hi,
I am trying to run Nanocaller using the command :
NanoCaller --bam _sorted.bam --ref ./sly.fa -chrom ch00 --mode snps --preset ont --cpu 64 --output Nano_Ch00 | tee stdout.txt

With the snp mode it runs through until variant calling mode and then throws this error

bcftools: symbol lookup error: /home/dnalinux/anaconda3/envs/bioenv/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

2022-09-01 18:59:01.609302: ------WhatsHap SNP phasing log------

This is WhatsHap 1.1 running under Python 3.9.6
Traceback (most recent call last):
  File "/home/dnalinux/anaconda3/envs/bioenv/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/home/dnalinux/anaconda3/envs/bioenv/lib/python3.9/site-packages/whatshap/__main__.py", line 83, in main
    module.main(args)
  File "/home/dnalinux/anaconda3/envs/bioenv/lib/python3.9/site-packages/whatshap/cli/phase.py", line 1107, in main
    run_whatshap(**vars(args))
  File "/home/dnalinux/anaconda3/envs/bioenv/lib/python3.9/site-packages/whatshap/cli/phase.py", line 338, in run_whatshap
    PhasedVcfWriter(
  File "/home/dnalinux/anaconda3/envs/bioenv/lib/python3.9/site-packages/whatshap/vcf.py", line 888, in __init__
    super().__init__(in_path, command_line, out_file, include_haploid_sets)
  File "/home/dnalinux/anaconda3/envs/bioenv/lib/python3.9/site-packages/whatshap/vcf.py", line 795, in __init__
    contigs, formats, infos = missing_headers(in_path)
  File "/home/dnalinux/anaconda3/envs/bioenv/lib/python3.9/site-packages/whatshap/vcf.py", line 700, in missing_headers
    with VariantFile(path) as variant_file:
  File "pysam/libcbcf.pyx", line 4036, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4266, in pysam.libcbcf.VariantFile.open
ValueError: invalid file `b'Nano_Ch001/variant_calls.snps.vcf.gz'` (mode=`b'r'`) - is it VCF/BCF format?

In the documentation it says whatshap is disabled by deafult. Not sure how to resolve this. I have attached my stdout file with this.
stdout.txt

I get the same error when I use mode 'all' as well.
@umahsn
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Collaborator

umahsn commented Sep 21, 2022

Hi,

I think there is some confusing language used on our behalf. Whatshap being disabled by default means that whatshap is disabled from changing genotypes during phasing. However, the problem here seems to be in bcftools, not whatshap, as shown by the error line bcftools: symbol lookup error: /home/dnalinux/anaconda3/envs/bioenv/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv which occurs before Whatshap is run. The raw VCF file output from NanoCaller is sorted by BCFtools

NanoCaller/nanocaller_src/snpCaller.py

Line 215 in 7823163

run_cmd("bcftools sort %s|bgziptabix %a" %(temp_output_file_path, output_file_path), error=True)

And the sorted/compressed VCF file is used by Whatshap. Since BCFtools is not working properly, it doesnt produce Nano_Ch001/variant_calls.snps.vcf.gz file, hence the error from Whatshap. Can you check if the BCFtools is working properly? You can run bcftools sort Nano_Ch001/variant_calls.snps.vcf manually to see if it works. It seems that uninstalling and then reinstalling BCFtools using the following commands can fix the issue with not finding the proper library files:

Uninstall:
conda uninstall bcftools

Reinstall:
conda install bcftools
or
conda install bcftools=1.14

@Arkadiy-Garber
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Just tried this fix, but continuing to get the same error. I installed NanoCaller using conda.

NanoCaller --bam GCA_027886375.1.nanopore.bam --ref GCA_027886375.1.fa --preset ont --output /data/MAB/3667/ --cpu 24

2023-08-01 19:33:22.504374: Starting NanoCaller.

NanoCaller command and arguments are saved in the following file: /data/MAB/3667/args

2023-08-01 19:33:22.910183: I tensorflow/core/util/port.cc:110] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2023-08-01 19:33:22.965992: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-08-01 19:33:23.838886: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
SNP Calling Progress: 100%|█████████████████████████████████████████████████████████████████████████████████████████| 25/25 [00:14<00:00,  1.72it/s]

2023-08-01 19:33:39.590770: Combining SNP calls.

2023-08-01 19:33:39.601264: Compressing and indexing SNP calls.
bcftools: symbol lookup error: /data/MAB/miniconda3/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

bcftools: symbol lookup error: /data/MAB/miniconda3/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv


2023-08-01 19:33:39.690194: SNP calling completed. Time taken= 14.6870

Indel Calling Progress:   0%|                                                                                                | 0/25 [00:00<?, ?it/s]

[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115655.1.phased.bam" : No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-52:
Process Process-43:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
Process Process-47:
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115655.1.phased.bam`: No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-37:
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-45:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Process Process-36:
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-42:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-31:
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Traceback (most recent call last):
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Process Process-34:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-50:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-49:
Process Process-30:
Process Process-44:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Process Process-41:
Traceback (most recent call last):
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-51:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Process Process-39:
Process Process-29:
Process Process-48:
Traceback (most recent call last):
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Traceback (most recent call last):
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Process Process-38:
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-40:
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-46:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-32:
Process Process-35:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
[E::hts_open_format] Failed to open file "/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam" : No such file or directory
Process Process-33:
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/MAB/miniconda3/envs/funannotate/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 262, in caller
    indel_run(params, indel_dict, job_Q, counter_Q, indel_files_list)
  File "/data/MAB/miniconda3/bin/nanocaller_src/indelCaller.py", line 69, in indel_run
    pos, x0_test, x1_test, x2_test, alleles_seq, phase = get_indel_testing_candidates(params, chunk)
  File "/data/MAB/miniconda3/bin/nanocaller_src/generate_indel_pileups.py", line 147, in get_indel_testing_candidates
    samfile = pysam.Samfile(sam_path, "rb")
  File "pysam/libcalignmentfile.pyx", line 747, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 946, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `/data/MAB/3667/intermediate_phase_files/CP115654.1.phased.bam`: No such file or directory
Indel Calling Progress:   0%|                                                                                                | 0/25 [00:01<?, ?it/s]

2023-08-01 19:33:41.163913: Compressing and indexing indel calls.
bcftools: symbol lookup error: /data/MAB/miniconda3/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv


2023-08-01 19:33:41.857258: Indel calling completed. Time taken= 2.1670


2023-08-01 19:33:41.857452: Total Time Elapsed: 19.35 seconds

@asmmahmoud
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asmmahmoud commented Sep 5, 2023 •
edited
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Hi,
I installed NanoCaller using conda and run it using this command: NanoCaller --bam /research/project/shared/benoukraf_lab/crc/bam/HRR698433.bam --ref /research/project/shared/benoukraf_lab/ref_hg38/UCSC_hg38.fa --output /research/project/shared/benoukraf_lab/crc/mut/HRR698433/ --cpu 10 --mode snps --preset ont
I couldn't view the output vcf file as shown below:
bcftools view variant_calls.snps.vcf.gz
bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

@umahsn
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umahsn commented Sep 5, 2023

Hi, this issue seems to be caused by bcftools installation, see samtools/bcftools/issues/1698 and here. It seems like this can be fixed by downgrading openssl as follows: conda install -c bioconda openssl=1.0

@ponomarevsy ponomarevsy mentioned this issue Oct 18, 2023
Closed
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@Arkadiy-Garber @umahsn @asmmahmoud @kprabhu-soundag