Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.010617
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.054441
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.067614
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.010937
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background
Finished invoke:
  name: bg  status: 0  time: 0.008548
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 363.977772
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 35.810539
Invoking:
  centrimo -seqlen 340 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.161323
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.383753
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary TAMCCACTRVRCCAHVNV /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.288222
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary CRCRYMWSVYTHNYAMBGWKRAGRTCMBSG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.267069
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary ARATGTAYGGRTGTWWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.261563
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary AASGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.175993
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary GGYTCGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.171854
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary CGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.176932
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary ACACTAK /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.170073
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary CGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.170552
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary CTATCACR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.165625
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary CGTGGMG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.1759
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.177213
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/spamo_out_12 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background -primary CAYACGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo12  status: 0  time: 0.165286
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif TAMCCACTRVRCCAHVNV /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.148521
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif CRCRYMWSVYTHNYAMBGWKRAGRTCMBSG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.15472
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif ARATGTAYGGRTGTWWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.15227
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif AASGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.052802
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif GGYTCGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.069726
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif CGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.065996
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif ACACTAK /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.053677
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif CGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.067963
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif CTATCACR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.068292
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif CGTGGMG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.067478
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.055797
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/background --motif CAYACGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo12  status: 0  time: 0.068497
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NOT3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.153256
Done