Invoking:
  getsize meme_out/cbf1_nit/cbf1.nit.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.085595
Invoking:
  fasta-most -min 50 < meme_out/cbf1_nit/cbf1.nit.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.098361
Invoking:
  fasta-center -dna -len 100 < meme_out/cbf1_nit/cbf1.nit.fa 1> meme_out/cbf1_nit/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.126943
Invoking:
  fasta-shuffle-letters meme_out/cbf1_nit/seqs-centered meme_out/cbf1_nit/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.031416
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 meme_out/cbf1_nit/cbf1.nit.fa meme_out/cbf1_nit/background
Finished invoke:
  name: bg  status: 0  time: 0.025742
Invoking:
  meme meme_out/cbf1_nit/seqs-centered -oc meme_out/cbf1_nit/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile meme_out/cbf1_nit/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 760.472102
Invoking:
  dreme -v 1 -oc meme_out/cbf1_nit/dreme_out -png -dna -p meme_out/cbf1_nit/seqs-centered -n meme_out/cbf1_nit/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 11.042895
Invoking:
  centrimo -seqlen 150 -verbosity 1 -oc meme_out/cbf1_nit/centrimo_out -bfile meme_out/cbf1_nit/background meme_out/cbf1_nit/cbf1.nit.fa meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.21303
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 meme_out/cbf1_nit/combined.meme meme_out/cbf1_nit/combined.meme 1> meme_out/cbf1_nit/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.065645
Invoking:
  spamo -verbosity 1 -oc meme_out/cbf1_nit/spamo_out_1 -bgfile meme_out/cbf1_nit/background -primary DRTCACGTGMW meme_out/cbf1_nit/cbf1.nit.fa meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.735307
Invoking:
  spamo -verbosity 1 -oc meme_out/cbf1_nit/spamo_out_2 -bgfile meme_out/cbf1_nit/background -primary RAAAAAAAAAAARAARAARAA meme_out/cbf1_nit/cbf1.nit.fa meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.457273
Invoking:
  spamo -verbosity 1 -oc meme_out/cbf1_nit/spamo_out_3 -bgfile meme_out/cbf1_nit/background -primary AAGAARGA meme_out/cbf1_nit/cbf1.nit.fa meme_out/cbf1_nit/dreme_out/dreme.xml meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.253319
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc meme_out/cbf1_nit/fimo_out_1 --bgfile meme_out/cbf1_nit/background --motif DRTCACGTGMW meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/cbf1.nit.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.244694
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc meme_out/cbf1_nit/fimo_out_2 --bgfile meme_out/cbf1_nit/background --motif RAAAAAAAAAAARAARAARAA meme_out/cbf1_nit/meme_out/meme.xml meme_out/cbf1_nit/cbf1.nit.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.256827
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc meme_out/cbf1_nit/fimo_out_3 --bgfile meme_out/cbf1_nit/background --motif AAGAARGA meme_out/cbf1_nit/dreme_out/dreme.xml meme_out/cbf1_nit/cbf1.nit.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.123376
Writing output
Invoking:
  meme-chip_html_to_tsv meme_out/cbf1_nit/meme-chip.html meme_out/cbf1_nit/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.215092
Done