Hi all, I'm having trouble getting my alignments recognized with PhastCons. I generated n alignments using lastz, did some filtering steps, and then used multiz n-1 times to get a file which are queries aligned to the same target. I generated a phylogenic tree with PhyloFit and this worked, but when I fed this all to phastCons, I'd get the following error: warning: maf_read: MAF file must be sorted with respect to reference sequence if store_order=TRUE. Ignoring out-of-order blocks maf.c:323: failed assertion `idx_offset >= 0' Abort trap
I used maf_order on the file taken as input to phastCons but I still got this error. I read somewhere that autoMZ can be used to generate a multiple alignment that respects phylogenic tree info but I am unable to see sample usage and the parameters are very vague. It looks like roast takes the same kind of parameters in the same order as autoMZ and I know that tool has been used for your data. Could you give me an example of how it's used? -- Bremen Braun _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
