Hi everybody,
when I run the build_profile_indexes.py script in the
scripts/tools/annotation_profiler/ directory on hg19 (downloaded
yesterday from UCSC), I get the following error:
Created table dir
(profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal).
['fileName']
Table wgEncodeOpenChromFaireGlioblaBaseOverlapSignal
(/galaxy/galaxy_data/ucsc_data/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.sql)
does not appear to have a chromosome, a start, or a stop.
Removing empty table (wgEncodeOpenChromFaireGlioblaBaseOverlapSignal)
directory
(profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal).
Created table dir
(profiled_annotations/hg19/wgEncodeCshlShortRnaSeqK562ChromatinShortTransfrags).
['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand',
'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount',
'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount',
'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount',
'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength',
'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY']
Traceback (most recent call last):
File
"/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py",
line 338, in <module>
if __name__ == "__main__": __main__()
File
"/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py",
line 310, in __main__
bitset_dict[ chrom ].set_range( start, end - start )
File "bitset.pyx", line 128, in bx.bitset.BitSet.set_range
(lib/bx/bitset.c:1130)
File "bitset.pyx", line 93, in bx.bitset.b_check_range_count
(lib/bx/bitset.c:656)
IndexError: End 16573 is larger than the size of this BitSet (16571).
Everything worked fine with mm9 and dm3.
Since the script wasn't changed in the last year, I suspect it has to do
with the UCSC data.
We don't really use hg19, so I'm fine with just leaving it out for now,
but I wanted to report the error anyway.
Best regards,
Sarah