Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.154538
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.068475
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.096787
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.032799
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.084361
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background
Finished invoke:
  name: bg  status: 0  time: 0.030159
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 981.493337
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 44.801203
Invoking:
  centrimo -seqlen 454 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.173273
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.479942
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary BSGGRATCGAACCSVGGACCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.528048
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary GSBYNYKTGGCCBAGTBGKTWRAGSSVHM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.457438
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.248333
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.447262
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary GCGCTWCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.221245
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary ACGATGGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.218042
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary CCGYGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.266589
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background -primary ACGCGAS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.220502
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif BSGGRATCGAACCSVGGACCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.417695
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif GSBYNYKTGGCCBAGTBGKTWRAGSSVHM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.423285
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.504564
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.28198
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif GCGCTWCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.318419
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif ACGATGGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.308103
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif CCGYGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.300285
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/background --motif ACGCGAS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/BY4742--STE12.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.295262
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.437876
Done