Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.026012
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.062062
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.080221
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.017001
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background
Finished invoke:
  name: bg  status: 0  time: 0.016642
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 738.125637
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 21.756008
Invoking:
  centrimo -seqlen 597 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.16073
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.287712
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background -primary AAAAAWYGMYCHMDMSSGGRATCGAACCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.435797
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background -primary SSCYTWAMCCACTVVGCYAHV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.399966
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background -primary TGWGRTGTAYGGRTGYR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.331587
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background -primary AAAAAADA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.286802
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background -primary CCAACTKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.189216
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background --motif AAAAAWYGMYCHMDMSSGGRATCGAACCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.296975
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background --motif SSCYTWAMCCACTVVGCYAHV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.279883
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background --motif TGWGRTGTAYGGRTGYR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.281895
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background --motif AAAAAADA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.214977
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/background --motif CCAACTKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/RM11-1A--CAD1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.192857
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.198303
Done