yeban
commented
7 years ago Sorry for slow response. Running gem install bio (or sudo gem install bio) should resolve that.
Closed sessmurda closed 7 years ago
yeban
commented
7 years ago Sorry for slow response. Running gem install bio (or sudo gem install bio) should resolve that.
Hi,
I was able to fix the previous error I posted about, but reached another in the final steps of processing on a sample run. I am unsure which database is missing, but I did receive the lifted/unlifted gff files which look reasonable so far. Any help finishing the last steps of the analysis would be greatly appreciated, log file copied below:
cat error.log nohup: ignoring input /global/u2/a/asession/SCRIPTS/flo/Rakefile:25: warning: Insecure world writable dir /global/common/genepool/usg/languages/R in PATH, mode 040777 mkdir run cp ./Chr1L.example/Chr1L.v91.fa run/source.fa cp ./Chr1L.example/Chr1L.v92.fa run/target.fa faToTwoBit run/source.fa run/source.2bit faToTwoBit run/target.fa run/target.2bit twoBitInfo run/source.2bit stdout | sort -k2nr > run/source.sizes twoBitInfo run/target.2bit stdout | sort -k2nr > run/target.sizes faSplit sequence run/target.fa 1 run/chunk_ parallel --joblog run/joblog.faSplit -j 1 -a run/joblst.faSplit 43201 pieces of 43961 written parallel --joblog run/joblog.blat -j 1 -a run/joblst.blat Loaded 219879705 letters in 1 sequences Searched 216002468 bases in 43201 sequences parallel --joblog run/joblog.liftUp -j 1 -a run/joblst.liftUp Got 43201 lifts in run/chunk_0.fa.lft Lifting run/chunk_0.fa.psl parallel --joblog run/joblog.axtChain -j 1 -a run/joblst.axtChain 693297 blocks after duplicate removal Loaded 219802468 bases of NC_030724.1 from run/target.2bit Loaded 219879705 bases of chr1L from run/source.2bit chainPair NC_030724.1-chr1L Main chaining step done in 2979 milliseconds 747068 blocks after duplicate removal chainPair NC_030724.1+chr1L Main chaining step done in 14412 milliseconds parallel --joblog run/joblog.chainSort -j 1 -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 1 chroms in run/source.sizes, 1 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 chr1L mkdir Chr1L-liftover-Chr1L.v92 liftOver -gff ./Chr1L.example/Chr1L.gff3 run/liftover.chn Chr1L-liftover-Chr1L.v92/lifted.gff3 Chr1L-liftover-Chr1L.v92/unlifted.gff3 Reading liftover chains Mapping coordinates WARNING: -gff is not recommended. Use 'ldHgGene -out=' and then 'liftOver -genePred '
rake aborted!
LoadError: cannot load such file -- bio/db/gff