Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.073562
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.0601
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.079315
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013512
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.065164
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background
Finished invoke:
  name: bg  status: 0  time: 0.019285
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 986.633858
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 48.701619
Invoking:
  centrimo -seqlen 320 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.288451
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.640806
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background -primary YCDGRAGRTCMBGGGTTCGAYYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.932655
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background -primary TTWDNAGTCWGRCGCBYTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.787137
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background -primary GGKCNHGTGGTSTAGTSGKTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.859772
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background -primary ARRAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.695651
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background -primary CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.759487
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background --motif YCDGRAGRTCMBGGGTTCGAYYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa
Finished invoke:
  name: fimo1  status: 0  time: 1.478816
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background --motif TTWDNAGTCWGRCGCBYTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa
Finished invoke:
  name: fimo2  status: 0  time: 1.44644
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background --motif GGKCNHGTGGTSTAGTSGKTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa
Finished invoke:
  name: fimo3  status: 0  time: 1.458673
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background --motif ARRAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa
Finished invoke:
  name: fimo4  status: 0  time: 1.262138
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/background --motif CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/YJM789--SOK2.fa
Finished invoke:
  name: fimo5  status: 0  time: 1.179752
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SOK2/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.338606
Done