Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.012182
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056071
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.068899
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.011509
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background
Finished invoke:
  name: bg  status: 0  time: 0.011253
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 520.366577
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 18.174271
Invoking:
  centrimo -seqlen 472 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.117749
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.560596
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background -primary AAAAAAAWYGVYCNMDVSSGGRWTCGAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.318497
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background -primary GGCCNRRTKGKTARSGCGYCNGACTHNWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.303361
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background -primary TAGTGTARYGGYTATCACHTYMCGYTTTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.242361
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background -primary CCAACW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.208561
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background -primary AAAAAADA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.226532
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background -primary AGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.207316
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background --motif AAAAAAAWYGVYCNMDVSSGGRWTCGAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.199726
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background --motif GGCCNRRTKGKTARSGCGYCNGACTHNWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.196267
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background --motif TAGTGTARYGGYTATCACHTYMCGYTTTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.198962
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background --motif CCAACW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.105429
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background --motif AAAAAADA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.133425
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/background --motif AGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/AWRI1631--NOT3.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.122256
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NOT3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.140809
Done