Closed calchoo closed 5 years ago
loading: /projects/wtss_scratch/mavis/POG/POG669/gd-P01759_gn-P01768_rd-P01763/mavis_v2.2.4/2010/P01759_diseased_genome/cluster/batch-TChGqiE6dfozYTTPbLwGMA-77.tab Traceback (most recent call last): File "/gsc/pipelines/mavis/v2.2.4/venv/bin/mavis", line 11, in <module> load_entry_point('mavis==2.2.4', 'console_scripts', 'mavis')() File "/gsc/pipelines/mavis/v2.2.4/venv/lib/python3.6/site-packages/mavis-2.2.4-py3.6.egg/mavis/main.py", line 414, in main raise err File "/gsc/pipelines/mavis/v2.2.4/venv/lib/python3.6/site-packages/mavis-2.2.4-py3.6.egg/mavis/main.py", line 371, in main validate_main.main(**args, start_time=start_time) File "/gsc/pipelines/mavis/v2.2.4/venv/lib/python3.6/site-packages/mavis-2.2.4-py3.6.egg/mavis/validate/main.py", line 86, in main cast={COLUMNS.cluster_id: lambda x: str(uuid()) if not x else x} File "/gsc/pipelines/mavis/v2.2.4/venv/lib/python3.6/site-packages/mavis-2.2.4-py3.6.egg/mavis/util.py", line 245, in read_inputs **kwargs File "/gsc/pipelines/mavis/v2.2.4/venv/lib/python3.6/site-packages/mavis-2.2.4-py3.6.egg/mavis/util.py", line 531, in read_bpp_from_input_file raise InvalidRearrangement('could not produce a valid rearrangement', row) mavis.error.InvalidRearrangement: ('could not produce a valid rearrangement', {'tracking_id': 'manta-MantaDEL:175574:0:0:0:0:0;strelka-8YtWsuCjhNRzCL2GN5pdbd', 'library': 'P01759', 'cluster_id': 'GicQ9HpSNkSQZ7woPVDYo2', 'cluster_size': '2', 'event_type': 'deletion', 'break1_chromosome': '15', 'break1_position_start': 67333604, 'break1_position_end': 67333604, 'break1_orientation': 'L', 'break1_strand': '?', 'break1_seq': None, 'break2_chromosome': '15', 'break2_position_start': 67333605, 'break2_position_end': 67333605, 'break2_orientation': 'R', 'break2_strand': '?', 'break2_seq': None, 'opposing_strands': False, 'stranded': False, 'protocol': 'genome', 'disease_status': 'diseased', 'tools': 'manta;strelka', 'untemplated_seq': None, 'BND_DEPTH': None, 'CIGAR': None, 'CONSENSUS': None, 'EVENT': None, 'Germline': None, 'HOMLEN': None, 'HOMSEQ': None, 'IC': None, 'IHP': None, 'IMPRECISE': None, 'INV3': None, 'INV5': None, 'JUNCTION_QUAL': None, 'JUNCTION_SOMATICSCORE': None, 'LEFT_SVINSSEQ': None, 'MAPQ': None, 'MATEID': None, 'MATE_BND_DEPTH': None, 'NT': None, 'OVERLAP': None, 'PE': None, 'PRECISE': None, 'QSI': None, 'QSI_NT': None, 'Quality': None, 'RC': None, 'RIGHT_SVINSSEQ': None, 'RU': None, 'SGT': None, 'SOMATIC': None, 'SOMATICSCORE': None, 'SR': None, 'SRQ': None, 'SVINSLEN': None, 'SVINSSEQ': None, 'SVLEN': None, 'SVMETHOD': None, 'Somatic': None, 'TQSI': None, 'TQSI_NT': None, 'id': None, 'line_no': 365, 'tag': None, 'transabyss_gene': None, 'transabyss_genes': None})
Manta 15 67333523 MantaDEL:175574:0:0:0:0:0 GGAAGGAAGGAAAAGGGAAGGGAAGGTAGAGAAGGAAGGAAAAGGGAAGGGAAGGTAGA G 89 MinGQ END=67333581;SVTYPE=DEL;SVLEN=-58;CIGAR=1M58D;CIPOS=0,96;HOMLEN=96;HOMSEQ=GAAGGAAGGAAAAGGGAAGGGAAGGTAGAGAAGGAAGGAAAAGGGAAGGGAAGGTAGAGAAGGAAGGAAAAGGGAAGGGAAGGTAGAGAAGGAAGG GT:FT:GQ:PL:PR:SR 0/1:MinGQ:3:139,3,0:0,0:0,4 Strelka 15 67333623 . AGG A . QSI_ref IC=1;IHP=4;NT=ref;QSI=12;QSI_NT=12;RC=3;RU=G;SGT=ref->het;SOMATIC;TQSI=2;TQSI_NT=2 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50 17:17:18,18:0,0:0,0:22.68:0.03:0.00 40:40:28,30:6,6:8,8:41.77:3.90:0.00
manta-MantaDEL:175574:0:0:0:0:0 deletion 15 67333523 67333619 L ? None 15 67333581 67333581 R ? None False False manta None 1M58D None 96 GAAGGAAGGAAAAGGGAAGGGAAGGTAGAGAAGGAAGGAAAAGGGAAGGGAAGGTAGAGAAGGAAGGAAAAGGGAAGGGAAGGTAGAGAAGGAAGG None None None None None None None None None None None None None -58 MantaDEL:175574:0:0:0:0:0 strelka-8YtWsuCjhNRzCL2GN5pdbd deletion 15 67333623 67333623 L ? None 15 67333625 67333625 R ? None False False strelka 1 4 ref None 12 12 3 G ref->het True 2 2
manta-MantaDEL:175574:0:0:0:0:0;strelka-8YtWsuCjhNRzCL2GN5pdbd sDpE4no2SeREAdspcg4zZU 2 deletion 15 67333604 67333604 L ? None 15 67333605 67333605 R ? None False False genome normal manta;strelka None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None None
related PR https://github.com/bcgsc/mavis/pull/194
MAVIS version: 2.2.4
Python version: 3.6.0
OS: Centos 6
Error
original inputs
converted inputs
Clustering output