Hi Sarah,

Sorry for the late reply. The error is related to a bug we're currently looking into. If you run it again, does it have this error consistently or does it only happen once in a while?

Thanks,

K

On Thu, Jul 7, 2011 at 12:11 PM, Sarah Diehl <diehl@immunbio.mpg.de> wrote:

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/ wgEncodeOpenChromFaireGlioblaB aseOverlapSignal).
['fileName']
Table wgEncodeOpenChromFaireGlioblaB aseOverlapSignal (/galaxy/galaxy_data/ucsc_ data/hg19/ wgEncodeOpenChromFaireGlioblaB aseOverlapSignal.sql) does not appear to have a chromosome, a start, or a stop.
Removing empty table ( wgEncodeOpenChromFaireGlioblaB aseOverlapSignal) directory (profiled_annotations/hg19/ wgEncodeOpenChromFaireGlioblaB aseOverlapSignal).
Created table dir (profiled_annotations/hg19/ wgEncodeCshlShortRnaSeqK562Chr omatinShortTransfrags).
['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
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