965  bash install_krakenuniq.sh -j
  966  ./install_krakenuniq.sh -j
  967  nano install_krakenuniq.sh 
  968  ./install_krakenuniq.sh "-j"
  969  ./install_krakenuniq.sh j
  970  ls
  971  cd j/
  972  ls
  973  cd ..
  974  rm -r j
  975  ls
  976  bash install_krakenuniq.sh -j
  977  cd ..
  978  wget http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz
  979  exit
  980  less README 
  981  ./configure 
  982  make -j 27
  983  make -j 27 check
  984  cd ../krakenuniq-0.5.8/
  985  ls
  986  bash install_krakenuniq.sh 
  987  bash install_krakenuniq.sh .
  988  ls
  989  pwd >> readme.txt
  990  nano readme.txt 
  991  exit
  992  /gscratch/srlab/programs/maker-2.31.10/bin/maker_map_ids --prefix OLUR_ --justify 8 20181127_oly_genome_snap02.all.noseqs.gff > 20180619_oly_genome.map
  993  mv 20180619_oly_genome.map 20190619_oly_genome.map
  994  /gscratch/srlab/programs/maker-2.31.10/bin/map_gff_ids -h
  995  ls
  996  /gscratch/srlab/programs/maker-2.31.10/bin/map_gff_ids 20190619_oly_genome.map 20181127_oly_genome_snap02.all.renamed.gff
  997  mv 20181127_oly_genome_snap02.all.noseqs.gff 20181127_oly_genome_snap02.all.renamed.gff
  998  /gscratch/srlab/programs/maker-2.31.10/bin/map_gff_ids 20190619_oly_genome.map 20181127_oly_genome_snap02.all.renamed.gff
  999  ls -ltrh
 1000  exit
 1001  /gscratch/srlab/programs/maker-2.31.10/bin/map_fasta_ids 20190619_oly_genome.map 20181127_oly_genome_snap02.all.maker.proteins.renamed.fasta 
 1002  /gscratch/srlab/programs/maker-2.31.10/bin/map_fasta_ids 20190619_oly_genome.map 20181127_oly_genome_snap02.all.maker.transcripts.renamed.fasta
 1003  rsync -av gannet:/volume2/web/Atumefaciens/20190108_oly_maker_blastp/20190108_blastp.outfmt6 .
 1004  ls -l
 1005  rsync -av /gscratch/srlab/blastdbs/UniProtKB_20190109/uniprot_sprot.fasta .
 1006  rsync -av gannet:/volume2/web/Atumefaciens/20190108_oly_maker_interproscan/20190108_oly_maker_proteins_ips.tsv .
 1007  /gscratch/srlab/programs/maker-2.31.10/bin/maker_functional_gff uniprot_sprot.fasta 20190108_blastp.outfmt6 20181127_oly_genome_snap02.all.renamed.gff > 20181127_oly_genome_snap02.all.renamed.putative_function.noseqs.gff
 1008  /gscratch/srlab/programs/maker-2.31.10/bin/ipr_update_gff 20181127_oly_genome_snap02.all.renamed.putative_function.noseqs.gff 20190108_oly_maker_proteins_ips.tsv > 20181127_oly_genome_snap02.all.renamed.putative_function.putative_domains.noseqs.gff 
 1009  ls -ltrh
 1010  rm 20181127_oly_genome_snap02.all.renamed.putative_function.putative_domains.noseqs.gff 
 1011  history
 1012  history | head
 1013  history | tail -n 50
 1014  history | tail -n 50 > command_history.txt