liftOver, invalid unsigned integer

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Anton Kratz

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May 27, 2016, 11:49:27 AM5/27/16
to gen...@soe.ucsc.edu
Dear UCSC team,

I am trying to lift over a bed12 file from hg19 to hg38, but get an "invalid unsigned integer" error.

I am using the liftOver binary downloaded from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver under Debian, and an overchain file downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz.

The command I run is:

time ./liftOver foobar.bed hg19ToHg38.over.chain hg38.foobar.bed hg38.unlifted.foobar.bed
Reading liftover chains
Mapping coordinates
invalid unsigned integer: (***)

(***) is the blockSizes field of the first entry of the bed12

best,
Anton

Brian Lee

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Jun 1, 2016, 1:20:58 AM6/1/16
to Anton Kratz, gen...@soe.ucsc.edu
Dear Anton,

Thank you for using the UCSC Genome Browser and your question about an error message when using liftOver.

Could you please provide some lines of the input file (foobar.bed) you are using. If the contents of '***' is representative of the file information for the blocksizes column, it could be your input file is incorrectly formatted as '***' is not a valid integer. You can send your data directly to me or to our private list at genom...@soe.ucsc.edu.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute
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