Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.017235
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.057048
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.072806
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.011929
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background
Finished invoke:
  name: bg  status: 0  time: 0.01467
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 775.747154
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 21.247207
Invoking:
  centrimo -seqlen 606 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.130013
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.399248
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background -primary GTCMBSGGTTCGATYCCSSKH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.446804
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background -primary GCBCARKTGGTAGMGCGYYAGACTYNWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.409042
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background -primary GGTNKYKTGGCCBAGTKGKTTAAGGCRYC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.298563
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background -primary AAAARWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.391137
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background -primary CGYGGAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.193746
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background --motif GTCMBSGGTTCGATYCCSSKH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.314503
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background --motif GCBCARKTGGTAGMGCGYYAGACTYNWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.316344
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background --motif GGTNKYKTGGCCBAGTKGKTTAAGGCRYC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.319932
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background --motif AAAARWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.237859
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/background --motif CGYGGAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/RM11-1A--PDR3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.223966
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.14267
Done