Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.043233
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.060145
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.099237
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.034923
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.083589
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background
Finished invoke:
  name: bg  status: 0  time: 0.034252
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 985.012926
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 62.243376
Invoking:
  centrimo -seqlen 501 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.168813
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.559159
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary YAABCDKRAGRTCMBSGGTTCGABYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.501186
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary TGGCCBAGTKGKTWRAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.468261
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary THDTCCGWKATAGTKTAAYGGYYAKMAYR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.318735
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary SAAGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.505762
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary CTTASC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.468063
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary CAACRATG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.267588
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.598223
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background -primary CCTGYAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.276908
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif YAABCDKRAGRTCMBSGGTTCGABYCCSVK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.427899
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif TGGCCBAGTKGKTWRAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.428133
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif THDTCCGWKATAGTKTAAYGGYYAKMAYR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.447373
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif SAAGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.298704
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif CTTASC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.301065
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif CAACRATG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.32522
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.3086
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/background --motif CCTGYAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/BY4742--MCM1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.323704
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MCM1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.472289
Done