Hi Kanwei,

the bug is consistent. I already tried it twice before I sent the bug report and just now I tried it again (also with updated data from UCSC), but I got the error again.


Best regards,
Sarah


On 08/24/2011 06:14 PM, Kanwei Li wrote:
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 <di...@immunbio.mpg.de <mailto:di...@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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