Invoking:
  getsize ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.027248
Invoking:
  fasta-most -min 50 < ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.093497
Invoking:
  fasta-center -dna -len 100 < ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa 1> ../meme_out/cbf1_nit_idr/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.119275
Invoking:
  fasta-shuffle-letters ../meme_out/cbf1_nit_idr/seqs-centered ../meme_out/cbf1_nit_idr/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.0137
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa ../meme_out/cbf1_nit_idr/background
Finished invoke:
  name: bg  status: 0  time: 0.013917
Invoking:
  meme ../meme_out/cbf1_nit_idr/seqs-centered -oc ../meme_out/cbf1_nit_idr/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile ../meme_out/cbf1_nit_idr/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 444.70044
Invoking:
  dreme -v 1 -oc ../meme_out/cbf1_nit_idr/dreme_out -png -dna -p ../meme_out/cbf1_nit_idr/seqs-centered -n ../meme_out/cbf1_nit_idr/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 11.149117
Invoking:
  centrimo -seqlen 341 -verbosity 1 -oc ../meme_out/cbf1_nit_idr/centrimo_out -bfile ../meme_out/cbf1_nit_idr/background ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.216477
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 ../meme_out/cbf1_nit_idr/combined.meme ../meme_out/cbf1_nit_idr/combined.meme 1> ../meme_out/cbf1_nit_idr/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.145435
Invoking:
  spamo -verbosity 1 -oc ../meme_out/cbf1_nit_idr/spamo_out_1 -bgfile ../meme_out/cbf1_nit_idr/background -primary WKCACGTGAYH ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.501042
Invoking:
  spamo -verbosity 1 -oc ../meme_out/cbf1_nit_idr/spamo_out_2 -bgfile ../meme_out/cbf1_nit_idr/background -primary THTWTWYTHNDHTTTTTTTTTTTWTTTTT ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.445498
Invoking:
  spamo -verbosity 1 -oc ../meme_out/cbf1_nit_idr/spamo_out_3 -bgfile ../meme_out/cbf1_nit_idr/background -primary TGRAAA ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa ../meme_out/cbf1_nit_idr/dreme_out/dreme.xml ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.405838
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc ../meme_out/cbf1_nit_idr/fimo_out_1 --bgfile ../meme_out/cbf1_nit_idr/background --motif WKCACGTGAYH ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.270074
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc ../meme_out/cbf1_nit_idr/fimo_out_2 --bgfile ../meme_out/cbf1_nit_idr/background --motif THTWTWYTHNDHTTTTTTTTTTTWTTTTT ../meme_out/cbf1_nit_idr/meme_out/meme.xml ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.295788
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc ../meme_out/cbf1_nit_idr/fimo_out_3 --bgfile ../meme_out/cbf1_nit_idr/background --motif TGRAAA ../meme_out/cbf1_nit_idr/dreme_out/dreme.xml ../meme_out/cbf1_nit_idr/cbf1.nit.idr.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.347272
Writing output
Invoking:
  meme-chip_html_to_tsv ../meme_out/cbf1_nit_idr/meme-chip.html ../meme_out/cbf1_nit_idr/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.217517
Done