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broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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problem dicing latest CN data (from 2018_06_13) #76

Closed noblem closed 5 years ago

noblem commented 6 years ago

2018-07-03 01:09:05,761[INFO]: Dicing file /xchip/gdac_data/gdc/mirror/TCGA/TCGA-ACC/Copy_Number_Variation/Copy_Number_Segment/BLAIN_p_TCGA_282_304_b2_N_GenomeWideSNP_6_D04_1348436.grch38.seg.v2.d38b4850-e280-433b-9964-b4371d8f82ba.txt 2018-07-03 01:09:05,827[ERROR]: Dicing FAILED: Traceback (most recent call last): File "/xchip/cga_home/mnoble/src/gdctools/gdctools/gdc_dice.py", line 226, in execute self.dice() File "/xchip/cga_home/mnoble/src/gdctools/gdctools/gdc_dice.py", line 170, in dice force=self.force) File "/xchip/cga_home/mnoble/src/gdctools/gdctools/gdc_dice.py", line 383, in dice_one convert(file_dict, mirror_path, dice_path) File "/xchip/cga_home/mnoble/src/gdctools/gdctools/lib/convert/seg.py", line 22, in process writeCsvFile(outfile, seg_file_data) File "/xchip/cga_home/mnoble/src/gdctools/gdctools/lib/common.py", line 155, in writeCsvFile csvfile.writerows(data) File "/xchip/cga_home/mnoble/src/gdctools/gdctools/lib/convert/seg.py", line 48, in generate_seg_file new_row = converter(row, tcga_id, hyb_id) File "/xchip/cga_home/mnoble/src/gdctools/gdctools/lib/convert/seg.py", line 89, in seg_broad if row['Sample'] != hyb_id: KeyError: 'Sample'

noblem commented 5 years ago

This was addressed in release v0.2.9