Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.019075
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058194
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.074487
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013251
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.063548
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background
Finished invoke:
  name: bg  status: 0  time: 0.014929
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1098.216318
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 33.82939
Invoking:
  centrimo -seqlen 496 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.15894
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.261853
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background -primary AAYCRDRRGRTCCBSGGTTCGATYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.561991
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background -primary GSBYNYKTGGCSHAGTGGKTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.547819
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background -primary TTTTTTTTTTTTTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.460517
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background -primary RCTATCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.250035
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background -primary GRAGAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.396964
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background -primary CCAACWG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.249837
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background --motif AAYCRDRRGRTCCBSGGTTCGATYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.362552
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background --motif GSBYNYKTGGCSHAGTGGKTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.357661
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background --motif TTTTTTTTTTTTTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.353455
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background --motif RCTATCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.262081
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background --motif GRAGAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.242155
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/background --motif CCAACWG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.238212
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.142605
Done