Hi Adnan, Thank you for sending more details about this issue. I forwarded this off to the developers. The update is that future versions of BLAT will reject databases with duplicated target database names (regardless of content).
The best solution for now is to simply avoid duplicating sequence names in the target database. Thank you, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/13/10 7:37 AM, Derti, Adnan wrote: > Hello. > > I'm using blat v. 32x1 in Linux. I got a bunch of core dumps and managed > to find a minimal combination of database& query sequences that cause > the error. The problem arises only if the database sequences have the > same ID, although this does not appear to be a sufficient condition. > Note that the db sequences in the case below are not identical, nor is > one a substring of the other; I think they're paralogs. > > Here's the error: > > blat: fuzzyFind.c:1438: ffFind: Assertion `hayStart<= hayEnd' failed. > Aborted > > Here's the query sequence: > >> qry > GGGATCATGCCCTGGGCTGAAGGCAGACACTCAACTGCTGAGCCACCCAGGTGCCCCCCTATAGTGGTAAGT > CTTAAAGGCAGGAGATCGGAAGAGCGTC > > Here are the db sequences: > >> db > TGGGGTGATTGGAGCTGTGATCTGGAGGAAGCAGCGCTCGGGAGGAAAAGGACCAGGCTACTCTCATGCTGC > ACGCGATGACAGTGCCCAGGGCTCTGATGTGTCTCTGACAGCTCCTAGAGTGTGAGACCAGCTGCCCTGTGG > GGACTGAGCGATGCAAGATGTGTTCACATCTCACGTGATGACATCAACAACCCTGGCTTGTCTCTGCAAACA > GTGTCAGGATGTGCCTGTGTCCCTAGGAGCATAATGTGAGGAGGTGGGGAGATTGGCCCACCCTGCCCACCA > TGACCTGTCCCTAATCTGATGTGCACTCTCTTCTCTGATGTGCTTTCCTGTCCAGCAGAGGGAGGGCTGGAC > CATCTCCATCCCTGTCTTTGTTTCATGTTGAGTACTAATAACTTACTACCCGATTGAAAATAAGAGGACAGG > GGTCCCTGGGTGGCCCAGCGCTTTAGCGCCGCCTTCAGCCCAGGGCATGATCCTGGAACCCGGGATCGAGTC > CCACATCGGGCTCC >> db > TGGGGTGATTGGAGCTGTGATCTGGAGGAAGCAGCGCTCGGGAGGAAAAGGACCAGGCTACTCTCATGCTGC > ACGTGATGACAGTGCCCAGGGCTCTGATGTGTCTCTGACAGCTCCTAGAGTGTGAGACCAGCTGCCCTGTGG > GGACTGAGCGATGCAAGATGTGTTCACATCTCACGTGATGACATCAACAACCCTGGCTTGTCTCTGCAAACA > GTGTCAGGATGTGCCTGTGTCCCTAGGAGCATAATGTGAGGAGGTGGGGAGATTGGCCCACCCTGCCCACCA > TGACCTGTCCCTAATCTGATGTGCGCTCTCTTCTCTGATGTGCTTTCCTGTCCAGGAGAGGGAGGGCTGGAC > CATCTCCATCCCTGTCTTTGTTTCATGTTGAGTACTAATGACTTACTACCCGATTGAAAATAAGAATCTTGG > GCAGCCCCAGTGGCTCAGCAGTTTAGCACCGCCTGCAGCCCAGGGCATGATCCTGGAACCCGGGATCGAATC > CCACATCGGGCTCCTGGGGTGATTGGAGCTGTGATCTGGAGGAAGCAGCGCTCGGGAGGAAAAGGACCAGGC > TACTCTCATGCTGCACGTGATGACAGTGCCCAGGGCTCTGATGTGTCTCTGACAGCTCCTAGAGTGTGAGAC > CAGCTGCCCTGTGGGGACTGAGCGATGCAAGATGTGTTCACATCTCACGTGATGACATCAACAACCCTGGCT > TGTCTCTGCAAACAGTGTCAGGATGTGCCTGTGTCCCTAGGAGCATAATGTGAGGAGGTGGGGAGATTGGCC > CACCCTGCCCACCATGACCTGTCCCTAATCTGATGTGCGCTCTCTTCTCTGATGTGCTTTCCTGTCCAGGAG > AGGGAGGGCTGGACCATCTCCATCCCTGTCTTTGTTTCATGTTGAGTACTAATGACTTACTACCCGATTGAA > AATAAGAATCCCGGTAGATCCCTGGGTGGCTCAGCGGTTTAGTGCCTGCCTTCAGCCCAGGGCA > TGATTCTGGAACCCGGGATCAAGTCCCACATCGGGCTCC > > Thanks. > > Adnan Derti > Notice: This e-mail message, together with any attachments, contains > information of Merck& Co., Inc. (One Merck Drive, Whitehouse Station, New > Jersey, USA 08889), and/or its affiliates Direct contact information for > affiliates is available at http://www.merck.com/contact/contacts.html) that > may be confidential, proprietary copyrighted and/or legally privileged. It is > intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and then > delete it from your system. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
