Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.017101
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.057995
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.074928
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013782
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.063572
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background
Finished invoke:
  name: bg  status: 0  time: 0.021554
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 986.090664
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 23.296212
Invoking:
  centrimo -seqlen 575 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.135237
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.357427
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background -primary VRMBSGGRATCGAACCSVGGAYCTYHYGV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.463604
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background -primary DTRGYBYAGTGGKTADVRSSYYMSVYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.525471
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background -primary TTYTTTTTTTTTTTTTTNKCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.383724
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background -primary ACGGTGM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.212167
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background --motif VRMBSGGRATCGAACCSVGGAYCTYHYGV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.343836
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background --motif DTRGYBYAGTGGKTADVRSSYYMSVYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.342399
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background --motif TTYTTTTTTTTTTTTTTNKCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.349925
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/background --motif ACGGTGM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/AWRI1631--NRG1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.2193
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--NRG1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.141006
Done