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wurmlab / flo

Same species annotation lift over pipeline.
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expecting number line 38 of gff3 #9

Closed olechnwin closed 7 years ago

olechnwin commented 7 years ago

Hi,

I am trying to liftover the ref_GRCh37.p13_top_level.gff3 to a denovo-assembled genome. but got the following error: mkdir ref_GRCh37.p13_top_level-liftover-A673_combined_fastq.1 liftOver -gff /gpfs0/home/rslssnck/cxt050/hg19/ref_GRCh37.p13_top_level.gff3 run/liftover.chn ref_GRCh37.p13_top_level-liftover-A673_combined_fastq.1/lifted.gff3 ref_GRCh37.p13_top_level-liftover-A673_combined_fastq.1/unlifted.gff3 Reading liftover chains Mapping coordinates WARNING: -gff is not recommended. Use 'ldHgGene -out=' and then 'liftOver -genePred ' Expecting number line 38 of /gpfs0/home/rslssnck/cxt050/hg19/ref_GRCh37.p13_top_level.gff3 rake aborted! Command failed with status (255): [liftOver -gff /gpfs0/home/rslssnck/cxt0...] /gpfs0/home/rslssnck/cxt050/opt/flo/Rakefile:232:in block (2 levels) in <top (required)>' /gpfs0/home/rslssnck/cxt050/opt/flo/Rakefile:223:ineach' /gpfs0/home/rslssnck/cxt050/opt/flo/Rakefile:223:in block in <top (required)>' /gpfs0/home/rslssnck/cxt050/.rvm/gems/ruby-2.4.0@global/gems/rake-12.0.0/exe/rake:27:in<top (required)>' Tasks: TOP => default (See full trace by running task with --trace)

I'm not sure what to do with this error. Your help is greatly appreciated. Thanks!

yeban commented 7 years ago

Looks like the input gff file is not valid. You can use genometools to check gff files (gt gff3 -sort -tidy -retainids ref_GRCh37.p13_top_level.gff3).