Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.013901
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056708
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.070125
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.011761
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background
Finished invoke:
  name: bg  status: 0  time: 0.013066
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 743.362116
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 30.876358
Invoking:
  centrimo -seqlen 349 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.125546
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.631331
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -primary DMBSGGRATCGAACCSVKGAYCTYCNSRTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.377357
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -primary SAAGAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.293846
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -primary ACCWCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.286756
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -primary CCRTACA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.190278
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -primary BTCCGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.18517
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -primary AAAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.30548
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background -primary AACTTGGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.184605
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background --motif DMBSGGRATCGAACCSVKGAYCTYCNSRTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.244661
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background --motif SAAGAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.13722
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background --motif ACCWCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.138696
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background --motif CCRTACA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.152198
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background --motif BTCCGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.153177
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background --motif AAAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.161677
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/background --motif AACTTGGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/YJM789--PDR3.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.15755
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.147023
Done