Error when using build_profile_indexes.py on hg19
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
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 ______________________________**_____________________________ 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:
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:
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Kanwei Li -
Sarah Diehl -
Sarah Diehl