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
