errors reported by axtchain

ucscGenomeBrowser / kent

UCSC Genome Browser source tree. Stable branch: "beta".

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errors reported by axtchain #85

Closed yeeus closed 7 months ago

yeeus commented 8 months ago

Describe the bug A clear and concise description of what the bug is.

NC_000005.10:110000000-120000000 is not in /path/to/GRCh38_noY.2bit

To Reproduce I followed the instruction on the website http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction to liftover the annotations on GRCh38 to my genome assembly. This error was produced to by axtchain in the Step 2 - chain/net.

Expected behavior Finally get the chain file.

Best wishes!

christopherLee1 commented 8 months ago

What are the chromosome names /path/to/GRCh38_noY.2bit? Something like this command will list the chromosomes: twoBitInfo /path/to/GRCh38_noY.2bit stdout

Also where did you get this 2bit file from? From our download server?

yeeus commented 7 months ago

I downloaded GRCh38 genome from NCBI and maybe axtchain read the record name rather than id like faTotwoBit.. I have solved this problem, thanks for your answer.