Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.054224
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.070011
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.088338
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.031598
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.083511
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background
Finished invoke:
  name: bg  status: 0  time: 0.019094
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1001.439284
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 22.41361
Invoking:
  centrimo -seqlen 483 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.156476
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.226775
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background -primary MBSGGRATCGAACCSVKGAYCTYCN /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.478283
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background -primary TWACCACTRVRCYAHVNVVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.510399
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background -primary RARAAAAARAAAAADAANAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.417475
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background --motif MBSGGRATCGAACCSVKGAYCTYCN /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.609082
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background --motif TWACCACTRVRCYAHVNVVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.421781
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/background --motif RARAAAAARAAAAADAANAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/AWRI1631--PHD1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.46574
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PHD1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.140992
Done