RPPA Issues

Owned by David Heiman
2015-10-13
1 min read

Annotation File Discrepancies

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SDRF Issues

Failure in fully processing sdrf file mdanderson.org_BRCA.MDA_RPPA_Core.mage-tab.1.3.0

/xchip/gdac_data/dcc_mirror3/dcc_site/tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/brca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BRCA.MDA_RPPA_Core.mage-tab.1.3.0/mdanderson.org_BRCA.MDA_RPPA_Core.sdrf.txt


protocol mdanderson.org:protein_normalization:01 failed in sdrf file column # 5 
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 124, in extractFilesFromSDRF
    file_info_bundle = fileBlock.getPerDataFileInfoAndFindUniqueFileBlockSamples()
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/FileBlock.py", line 94, in getPerDataFileInfoAndFindUniqueFileBlockSamples
    "\n\t%s %s %s" % (hyb2tcga_dict[hyb_id],hyb_id,existingFileSubpath))
Exception: Unable to filter conflicting lines in sdrf file:
        TCGA-A1-A0SF-01A-21-A17I-20 f0b3d871-c0aa-4ef8-ab74-c3e812393ed5 ../mdanderson.org_BRCA.MDA_RPPA_Core.Level_3.3.0.0/mdanderson.org_BRCA.MDA_RPPA_Core.protein_expression.Level_3.f0b3d871-c0aa-4ef8-ab74-c3e812393ed5.txt
        TCGA-A1-A0SF-01A-21-A17I-20 f0b3d871-c0aa-4ef8-ab74-c3e812393ed5 ../mdanderson.org_BRCA.MDA_RPPA_Core.Level_3.2.0.0/mdanderson.org_BRCA.MDA_RPPA_Core.protein_expression.Level_3.f0b3d871-c0aa-4ef8-ab74-c3e812393ed5.txt
Failure in fully processing sdrf file mdanderson.org_SKCM.MDA_RPPA_Core.mage-tab.1.6.0

/xchip/gdac_data/dcc_mirror3/dcc_site/tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/skcm/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_SKCM.MDA_RPPA_Core.mage-tab.1.6.0/mdanderson.org_SKCM.MDA_RPPA_Core.sdrf.txt


protocol mdanderson.org:protein_normalization:01 failed in sdrf file column # 5 
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 124, in extractFilesFromSDRF
    file_info_bundle = fileBlock.getPerDataFileInfoAndFindUniqueFileBlockSamples()
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/FileBlock.py", line 94, in getPerDataFileInfoAndFindUniqueFileBlockSamples
    "\n\t%s %s %s" % (hyb2tcga_dict[hyb_id],hyb_id,existingFileSubpath))
Exception: Unable to filter conflicting lines in sdrf file:
        TCGA-BF-A1PU-01A-21-A20M-20 7E74CAFD-C47B-4F98-A349-BBD2AC699D2D ../mdanderson.org_SKCM.MDA_RPPA_Core.Level_3.2.0.0/mdanderson.org_SKCM.MDA_RPPA_Core.protein_expression.Level_3.7E74CAFD-C47B-4F98-A349-BBD2AC699D2D.txt
        TCGA-BF-A1PU-01A-21-A20M-20 7E74CAFD-C47B-4F98-A349-BBD2AC699D2D ../mdanderson.org_SKCM.MDA_RPPA_Core.Level_3.1.4.0/mdanderson.org_SKCM.MDA_RPPA_Core.protein_expression.Level_3.7E74CAFD-C47B-4F98-A349-BBD2AC699D2D.txt
Fatal error processing sdrf file mdanderson.org_THCA.MDA_RPPA_Core.mage-tab.1.2.0

/xchip/gdac_data/dcc_mirror3/dcc_site/tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/thca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_THCA.MDA_RPPA_Core.mage-tab.1.2.0/mdanderson.org_THCA.MDA_RPPA_Core.sdrf.txt


Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 110, in extractFilesFromSDRF
    fileBlockSamplesDict = self._getFileBlockSamplesDict(headerBlock, dcc_mirror_dirs)
  File "build/bdist.linux-x86_64/egg/gdac_lib/sdrf/SDRFProcessor.py", line 231, in _getFileBlockSamplesDict
    raise Exception(error_msg)
Exception: Protocol REF entry mdanderson.org:antibody_probe:02 is not consistent with prior entry mdanderson.org:antibody_probe:01