Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.021535
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.057047
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.071828
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.019871
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background
Finished invoke:
  name: bg  status: 0  time: 0.020277
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 757.044276
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 18.27977
Invoking:
  centrimo -seqlen 457 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.122213
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.186681
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background -primary CDMBSGGRRTCGAACCSVKGAYCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.334359
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background -primary GSBYNYDTGGYYYAGTKGKTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.367821
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background -primary VGRTGTATGGRTGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.257198
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background --motif CDMBSGGRRTCGAACCSVKGAYCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.289091
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background --motif GSBYNYDTGGYYYAGTKGKTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.259114
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/background --motif VGRTGTATGGRTGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/BY4741--NOT3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.25005
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--NOT3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.136703
Done