Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.092593
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.067905
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.079846
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.020873
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background
Finished invoke:
  name: bg  status: 0  time: 0.016292
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 690.337177
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 27.212826
Invoking:
  centrimo -seqlen 567 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.151584
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.345899
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary GRATCGAACCSVKGAYCTYMNGRTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.468851
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary GNNSSCTYWAMCMACTRRRCYAHVRVRSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.497889
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary CAYCCRTACAYCHYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.417921
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary AAGAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.445277
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.244786
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary AGAYCGGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.222308
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary ACCAACTK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.231966
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background -primary AAWAAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.493843
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif GRATCGAACCSVKGAYCTYMNGRTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.27255
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif GNNSSCTYWAMCMACTRRRCYAHVRVRSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.263978
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif CAYCCRTACAYCHYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.251628
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif AAGAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.157608
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.163965
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif AGAYCGGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.181538
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif ACCAACTK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.181535
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/background --motif AAWAAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/YJM789--CUP9.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.160844
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.182753
Done