Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.01298
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056279
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.071676
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012258
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background
Finished invoke:
  name: bg  status: 0  time: 0.012969
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 623.755899
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 29.909802
Invoking:
  centrimo -seqlen 682 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.122913
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.31516
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary CDDRAGRTCMBGGGTTCGAYYCCSVKHGDG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.392098
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary DTRGYBYAGTGGKTARAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.41763
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary CACCCRTACAYCNYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.334473
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary AAAAAAAD /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.331306
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.186017
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary KCACGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.173931
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary CCAASAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.181935
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background -primary AGMGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.244312
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif CDDRAGRTCMBGGGTTCGAYYCCSVKHGDG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.237228
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif DTRGYBYAGTGGKTARAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.223348
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif CACCCRTACAYCNYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.216851
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif AAAAAAAD /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.14405
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.134929
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif KCACGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.144355
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif CCAASAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.139739
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/background --motif AGMGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/YJM789--AFT2.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.138887
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--AFT2/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.146572
Done