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 <diehl@immunbio.mpg.de mailto: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
______________________________ _____________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/