wurmlab / flo

Same species annotation lift over pipeline.
96 stars 28 forks source link

GFF format issue with CoGe input #42

Open splaisan opened 1 year ago

splaisan commented 1 year ago

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