Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.054784
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.060836
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.079478
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.015347
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.067249
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background
Finished invoke:
  name: bg  status: 0  time: 0.018023
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1004.48203
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 47.801887
Invoking:
  centrimo -seqlen 447 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.136935
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.62108
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary AAYCSDRRGGTCCBSGGTTCGATYCCSVGH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.428949
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary WHARKCBKRYGCCTTAACCAACTKGGCCAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.356671
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary AAARCSKRAWGTGATARCCRYTACACTATA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.292199
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary AARAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.418477
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary AGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.309618
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary ATCTKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.432072
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary CRACAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.456894
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary TCTMCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.276973
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background -primary CACCGTGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.246862
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif AAYCSDRRGGTCCBSGGTTCGATYCCSVGH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.480894
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif WHARKCBKRYGCCTTAACCAACTKGGCCAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.485409
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif AAARCSKRAWGTGATARCCRYTACACTATA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.486167
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif AARAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.383283
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif AGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.349612
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif ATCTKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.336019
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif CRACAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.3356
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif TCTMCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.342803
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/background --motif CACCGTGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/AWRI1631--SOK2.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.365361
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--SOK2/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.177001
Done