HI
I am trying to liftover a GFF genome annotation but fail to get the GFF accepted by the software.
Here is a minimal sample that triggers the crash
1 CoGe transcript 8522 12619 . + . transcript_id "C00s001g005000.mRNA1"; gene_id "C00s001g005000"; gene_name "C00s001g005000";
I run the following command using the latest docker and all inputs are present
docker run --rm --user "$(id -u):$(id -g)" \
-v $PWD:/workdir \
informationsea/transanno:latest transanno minimap2chain \
/workdir/${pfxq}_to_${pfxt}.paf \
--output /workdir/${pfxq}_to_${pfxt}.chain
I get
nom error: Error(("transcript_id \"C00s001g005000.mRNA1\"; gene_id \"C00s001g005000\"; gene_name \"C00s001g005000\";\n", CrLf))
thread 'main' panicked at 'Operation Error: LiftOverError { inner: GeneParseError { inner: GeneParseError { inner:
Parse error }
Parse error at line: 1 }
Failed to parse gene annotation }', transanno/src/main.rs:30:13
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
I could not figure how to add RUST_BACKTRACE=1 to a docker call
Thanks for your help
HI
I am trying to liftover a GFF genome annotation but fail to get the GFF accepted by the software.
Here is a minimal sample that triggers the crash
I run the following command using the latest docker and all inputs are present
I get
I could not figure how to add
RUST_BACKTRACE=1to a docker callThanks for your help