Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.016103
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.057077
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.072401
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013668
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.091266
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background
Finished invoke:
  name: bg  status: 0  time: 0.012563
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 879.031239
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 89.435365
Invoking:
  centrimo -seqlen 480 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.192416
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.289204
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary SSCYTWAMCCACTNSGCCAHR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.623125
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary GRTCMBSGGTTCGAYYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.655582
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary HACAYCCRTACAYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.501476
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary ARAAAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.588459
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.257471
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.32829
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary CGTWGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.252793
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary CCGATGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.228453
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary GMTTAACA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.27461
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary GGTCTCY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.263924
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary AGTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.231035
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/spamo_out_12 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background -primary CGGTGAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo12  status: 0  time: 0.23481
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif SSCYTWAMCCACTNSGCCAHR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.270175
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif GRTCMBSGGTTCGAYYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.267169
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif HACAYCCRTACAYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.258203
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif ARAAAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.148312
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.164855
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.187477
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif CGTWGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.161925
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif CCGATGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.162777
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif GMTTAACA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.16239
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif GGTCTCY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.162613
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif AGTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.164492
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif CGGTGAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
Finished invoke:
  name: fimo12  status: 0  time: 0.164809
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.156178
Done