cram files

[SanVerb]

Hello

I was wondering if there are any plans in the future to support cram files as input?

From my understanding, clair3nova does not support cram files at the moment. :)

Kind regards

Sanché Verbeeck

[SanVerb]

Hello,

My apologies!! I found out that providing .bai files with your cram files is enough to run the workflow.

However, I do get the following information in the log file:

.... (only last part of log file is shown) ....
INFO:root:Finish!
Total processed positions in chr15 (chunk 1/1) : 894

real    0m36.314s
user    0m42.804s
sys 0m6.069s
Traceback (most recent call last):
  File "/home/sverbeeck/DEEMPRINT/Clair3-Nova/trio/../clair3.py", line 115, in <module>
    main()
  File "/home/sverbeeck/DEEMPRINT/Clair3-Nova/trio/../clair3.py", line 102, in main
    submodule = import_module("%s.%s" % (directory, submodule_name))
  File "/home/sverbeeck/DEEMPRINT/.snakemake/conda/e7106693c564ec64c965e27eb3736d9d_/lib-python/3/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1003, in _gcd_import
  File "<frozen importlib._bootstrap>", line 980, in _find_and_load
  File "<frozen importlib._bootstrap>", line 964, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 674, in _load_unlocked
  File "<builtin>/frozen importlib._bootstrap_external", line 687, in exec_module
  File "<builtin>/frozen importlib._bootstrap_external", line 794, in get_code
  File "<builtin>/frozen importlib._bootstrap_external", line 754, in source_to_code
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "<string>", line 249
    print("[INFO] compressing and indexing GVCF files ...")
    ^
TabError: inconsistent use of tabs and spaces in indentation
Traceback (most recent call last):
  File "/home/sverbeeck/DEEMPRINT/Clair3-Nova/trio/../clair3.py", line 115, in <module>
    main()
  File "/home/sverbeeck/DEEMPRINT/Clair3-Nova/trio/../clair3.py", line 102, in main
    submodule = import_module("%s.%s" % (directory, submodule_name))
  File "/home/sverbeeck/DEEMPRINT/.snakemake/conda/e7106693c564ec64c965e27eb3736d9d_/lib-python/3/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1003, in _gcd_import
  File "<frozen importlib._bootstrap>", line 980, in _find_and_load
  File "<frozen importlib._bootstrap>", line 964, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 674, in _load_unlocked
  File "<builtin>/frozen importlib._bootstrap_external", line 687, in exec_module
  File "<builtin>/frozen importlib._bootstrap_external", line 794, in get_code
  File "<builtin>/frozen importlib._bootstrap_external", line 754, in source_to_code
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "<string>", line 249
    print("[INFO] compressing and indexing GVCF files ...")
    ^
TabError: inconsistent use of tabs and spaces in indentation
Traceback (most recent call last):
  File "/home/sverbeeck/DEEMPRINT/Clair3-Nova/trio/../clair3.py", line 115, in <module>
    main()
  File "/home/sverbeeck/DEEMPRINT/Clair3-Nova/trio/../clair3.py", line 102, in main
    submodule = import_module("%s.%s" % (directory, submodule_name))
  File "/home/sverbeeck/DEEMPRINT/.snakemake/conda/e7106693c564ec64c965e27eb3736d9d_/lib-python/3/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1003, in _gcd_import
  File "<frozen importlib._bootstrap>", line 980, in _find_and_load
  File "<frozen importlib._bootstrap>", line 964, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 674, in _load_unlocked
  File "<builtin>/frozen importlib._bootstrap_external", line 687, in exec_module
  File "<builtin>/frozen importlib._bootstrap_external", line 794, in get_code
  File "<builtin>/frozen importlib._bootstrap_external", line 754, in source_to_code
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "<string>", line 249
    print("[INFO] compressing and indexing GVCF files ...")
    ^
TabError: inconsistent use of tabs and spaces in indentation

real    2m43.180s
user    4m34.766s
sys 0m37.726s

It seems there is a typo in file: Clair3-Nova/trio/SortVcf_Trio.py

It could be that I accidently caused the typo, but I don't remember editing anything in this file so I mention it here in any case.

Kind regards

Sanché Verbeeck

[sujunhao]

Hi Sanché Verbeeck,

Thanks for your information. I confirmed that the typo is in the source file, and I fixed it in the latest version in this repo, hope you can finally run the tool successfully.

Regards, JH