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How to get ReCapSeg?

LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

Please email: [email protected]

Instructions will be sent and a download link, with instructions, will be provided.

ReCapSeg is free for non-profit users.

Comments

  • egeulgenegeulgen USMember

    @LeeTL1220 Hey I successfully downloaded and set up ReCapseg following your instructions.
    I'm trying to run the proportional coverage but am getting the following error:

    (recapseg)13645069790:NOT-0049 koray$ recapseg pc ./ReCapSeg/"$normal_name"/"$normal_name".coverage ../SeqCapv2.bed tmp_rg_mapping ./ReCapSeg/"$normal_name"/"$normal_name".recapseg.pc
    2015-08-10 16:57:23,560 INFO [capseg.tools.recapseg.recapseg:212] Version: 1.4.4.0
    2015-08-10 16:57:23,561 INFO [capseg.tools.recapseg.recapseg:213] Args: Namespace(func=, interval_bed_filename='../SeqCapv2.bed', is_debug=False, log_name='recapseg.log', output_proportional_coverage_file_basename='./ReCapSeg/NOT-0049-01/NOT-0049-01.recapseg.pc', raw_coverage_file='./ReCapSeg/NOT-0049-01/NOT-0049-01.coverage', readgroup_percent_zero_filter=1.0, sample_read_group_filename='tmp_rg_mapping')
    2015-08-10 16:57:23,561 INFO [capseg.tools.recapseg.recapseg:214] Log file: /Users/koray/WEX/NOT_july15/NOT-0049/recapseg.log
    2015-08-10 16:57:23,562 INFO [capseg.tools.recapseg.recapseg:44] Running Proportional Coverage: Namespace(func=, interval_bed_filename='../SeqCapv2.bed', is_debug=False, log_name='recapseg.log', output_proportional_coverage_file_basename='./ReCapSeg/NOT-0049-01/NOT-0049-01.recapseg.pc', raw_coverage_file='./ReCapSeg/NOT-0049-01/NOT-0049-01.coverage', readgroup_percent_zero_filter=1.0, sample_read_group_filename='tmp_rg_mapping')
    2015-08-10 16:57:23,562 INFO [capseg.Capsegger:97] Starting proportional coverage calculation...
    Traceback (most recent call last):
    File "/Users/koray/recapseg/bin/recapseg", line 9, in
    load_entry_point('recapseg==1.4.4.0', 'console_scripts', 'recapseg')()
    File "/Users/koray/recapseg/lib/python2.7/site-packages/recapseg-1.4.4.0-py2.7.egg/capseg/tools/recapseg/recapseg.py", line 217, in main
    args.func(args)
    File "/Users/koray/recapseg/lib/python2.7/site-packages/recapseg-1.4.4.0-py2.7.egg/capseg/tools/recapseg/recapseg.py", line 49, in process_pc
    args.readgroup_percent_zero_filter)
    File "/Users/koray/recapseg/lib/python2.7/site-packages/recapseg-1.4.4.0-py2.7.egg/capseg/Capsegger.py", line 101, in run_proportional_coverage
    index_col=[3])
    File "/Users/koray/recapseg/lib/python2.7/site-packages/pandas/io/parsers.py", line 474, in parser_f
    return _read(filepath_or_buffer, kwds)
    File "/Users/koray/recapseg/lib/python2.7/site-packages/pandas/io/parsers.py", line 250, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
    File "/Users/koray/recapseg/lib/python2.7/site-packages/pandas/io/parsers.py", line 566, in __init__
    self._make_engine(self.engine)
    File "/Users/koray/recapseg/lib/python2.7/site-packages/pandas/io/parsers.py", line 705, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
    File "/Users/koray/recapseg/lib/python2.7/site-packages/pandas/io/parsers.py", line 1126, in __init__
    self.index_col)
    File "/Users/koray/recapseg/lib/python2.7/site-packages/pandas/io/parsers.py", line 2214, in _clean_index_names
    name = cp_cols[c]
    IndexError: list index out of range

    I tried reinstalling pandas, thinking this might be a problem with the version, but I keep getting the same error.

    Looking forward to your further assistance,
    Best,
    -E

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

    @egeulgen Apologies for the delay in getting back to you. I just saw this message. Which version of pandas are you using? You can find out with a pip freeze. We have actually had issues with later versions of pandas. We have pegged recapseg to pandas==0.14.1. Are you using the create_recapseg_venv.sh in scripts/? If not, you should. This will create a python virtual environment with the exact versions that we run (en masse) at the Broad.

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

    @egeulgen If you are not using pandas 0.14.1, you can install it with pip install pandas==0.14.1

  • nutechunutechu Member

    Hello
    I didn't success run recapseg proportional coverage even using virtual environment.. I checked version of pandas and it's also exactly the same as recommend (version 0.14.1) ..I could run test script without any error ( $ nosetests --all-modules --exe -w test -v --processes=4 --process-timeout=480 --process-restartworker)

    here is my error (exactly match with above comment)

    2015-12-03 13:59:40,519 INFO [capseg.tools.recapseg.recapseg:212] Version: 1.4.4.0
    2015-12-03 13:59:40,520 INFO [capseg.tools.recapseg.recapseg:213] Args: Namespace(func=, interval_bed_filename='/home/ubuntu/data/sort_TargetSeq_exome_target_regions_hg19.bed', is_debug=False, log_name='recapseg.log', output_proportional_coverage_file_basename='RS122003_B', raw_coverage_file='RS122003_B.tsv', readgroup_percent_zero_filter=1.0, sample_read_group_filename='tmp_rg_mapping')
    2015-12-03 13:59:40,520 INFO [capseg.tools.recapseg.recapseg:214] Log file: /home/ubuntu/data/recapseg.log
    2015-12-03 13:59:40,520 INFO [capseg.tools.recapseg.recapseg:44] Running Proportional Coverage: Namespace(func=, interval_bed_filename='/home/ubuntu/data/sort_TargetSeq_exome_target_regions_hg19.bed', is_debug=False, log_name='recapseg.log', output_proportional_coverage_file_basename='RS122003_B', raw_coverage_file='RS122003_B.tsv', readgroup_percent_zero_filter=1.0, sample_read_group_filename='tmp_rg_mapping')
    2015-12-03 13:59:40,520 INFO [capseg.Capsegger:97] Starting proportional coverage calculation...
    Traceback (most recent call last):
    File "/usr/local/bin/recapseg", line 9, in
    load_entry_point('recapseg==1.4.4.0', 'console_scripts', 'recapseg')()
    File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg
    217, in main
    args.func(args)
    File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg
    49, in process_pc
    args.readgroup_percent_zero_filter)
    File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg
    roportional_coverage
    index_col=[3])
    File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 452,
    return _read(filepath_or_buffer, kwds)
    File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 234,
    parser = TextFileReader(filepath_or_buffer, **kwds)
    File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 542,
    self._make_engine(self.engine)
    File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 679,
    self._engine = CParserWrapper(self.f, **self.options)
    File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 1095,
    self.index_col)
    File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 2134,
    name = cp_cols[c]
    IndexError: list index out of range

    Hope anyone help.. I could not figure it out why..
    Thank you very much

  • nutechunutechu Member

    @LeeTL1220
    I would like to tag you to see my question.. sorry to disturb..
    and looking for your recommendation.
    thank you

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

    @nutechu Apologies for the late reply. There are quite a few possible problems. Most likely, the target file used for the coverage collection does not match the one used for the proportinoal coverage.

    Also, we are going to phase out ReCapSeg in favor of GATK CNV, which implements most of the functinoality of ReCapSeg. GATK CNV is also much easier to install, deploy, and debug if an error does occur. And GATK CNV is faster, too.

    @Geraldine_VdAuwera will have more information.

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