Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.060044
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.057947
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.076204
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.018612
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.07941
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background
Finished invoke:
  name: bg  status: 0  time: 0.019591
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1002.610858
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 26.208821
Invoking:
  centrimo -seqlen 532 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.151349
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.546015
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background -primary CDMSSGGRATCGAACCSVBGAYCTYCNGV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.465448
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background -primary WGSBBNYKTGGCSBAGTGGKWWARGSSHNC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.503664
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background -primary CCAAMAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.227194
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background -primary CTTACCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.253364
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background -primary ARAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.362207
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background --motif CDMSSGGRATCGAACCSVBGAYCTYCNGV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.390885
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background --motif WGSBBNYKTGGCSBAGTGGKWWARGSSHNC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.392599
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background --motif CCAAMAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.26584
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background --motif CTTACCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.251772
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/background --motif ARAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/RM11-1A--CUP2.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.230807
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CUP2/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.178877
Done