Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.015272
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056976
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.07136
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012614
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background
Finished invoke:
  name: bg  status: 0  time: 0.012998
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 857.998648
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 25.990089
Invoking:
  centrimo -seqlen 571 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.135969
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.431562
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary CVDCSSGGRATCGAACCSVGGACCTYH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.506441
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary TRGYYYAGTKGKTWRAGSSNNCGR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.507454
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary CGGTGARARCGTGATGTGATAGCCGTTAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.263692
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary CCWTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.233731
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.467406
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary ACCWCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.415693
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.47382
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background -primary ACTGGGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.239551
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif CVDCSSGGRATCGAACCSVGGACCTYH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.289108
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif TRGYYYAGTKGKTWRAGSSNNCGR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.282417
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif CGGTGARARCGTGATGTGATAGCCGTTAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.290613
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif CCWTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.194123
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.199514
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif ACCWCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.174984
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.173148
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/background --motif ACTGGGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.187503
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.147711
Done