parallel --joblog run/joblog.chainSort -j 15 -a run/joblst.chainSort
chainMergeSort run/*.chn.sorted | chainSplit run stdin -lump=1
mv run/000.chain run/combined.chn.sorted
chainNet run/combined.chn.sorted run/source.sizes run/target.sizes run/combined.chn.sorted.net /dev/null
Got 15 chroms in run/source.sizes, 15 in run/target.sizes
Finishing nets
writing run/combined.chn.sorted.net
writing /dev/null
netChainSubset run/combined.chn.sorted.net run/combined.chn.sorted run/liftover.chn
Processing 1
Processing 5
Processing 2
Processing 3
Processing 11
Processing 6
Processing 7
Processing 8
Processing 9
Processing 4
Processing 10
Processing 14
Processing 12
Processing 13
Processing MT
mkdir run/h99_longest_transcript
liftOver -gff /scratch/mblab/chasem/liftOver/flo_crypto/h99/h99_longest_transcript.gff run/liftover.chn run/h99_longest_transcript/lifted.gff3 run/h99_longest_transcript/unlifted.gff3
Reading liftover chains
Mapping coordinates
WARNING: -gff is not recommended.
Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'
/scratch/mblab/chasem/liftOver/flo/gff_recover.rb run/h99_longest_transcript/lifted.gff3 2> run/h99_longest_transcript/lifted_cleanup.log | gt gff3 -tidy -sort -addids -retainids - > run/h99_longest_transcript/lifted_cleaned.gff 2>> run/h99_longest_transcript/lifted_cleanup.log
rake aborted!
Command failed with status (1): [/scratch/mblab/chasem/liftOver/flo/gff_rec...]
/scratch/mblab/chasem/liftOver/flo/Rakefile:60:in `block (2 levels) in <top (required)>'
/scratch/mblab/chasem/liftOver/flo/Rakefile:40:in `each'
/scratch/mblab/chasem/liftOver/flo/Rakefile:40:in `block in <top (required)>'
Tasks: TOP => default