Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.056844
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.062145
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.085036
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.037711
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.079989
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background
Finished invoke:
  name: bg  status: 0  time: 0.020992
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 968.818739
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 65.443228
Invoking:
  centrimo -seqlen 410 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.265278
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.455736
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary DTGGCCVAGTKGKTWARGSG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.313959
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary SGGRVTCGAACCCVKGACCYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.295201
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.288455
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary CGCCASAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.20677
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary GMTACCGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.196636
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary ATYGTTGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.180275
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary ATACAACW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.173796
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary CGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.216834
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary AGACCAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.185026
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary CCRTGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.177881
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary ACGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.402565
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/spamo_out_12 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background -primary AAGGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo12  status: 0  time: 0.186757
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif DTGGCCVAGTKGKTWARGSG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.225834
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif SGGRVTCGAACCCVKGACCYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.214552
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.123379
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif CGCCASAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.136624
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif GMTACCGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.13933
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif ATYGTTGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.149018
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif ATACAACW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.161124
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif CGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.150026
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif AGACCAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.148211
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif CCRTGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.142372
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif ACGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.127726
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/background --motif AAGGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/BY4742--YAP1.fa
Finished invoke:
  name: fimo12  status: 0  time: 0.118263
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YAP1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.245891
Done