Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.019042
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058343
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.074946
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013944
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.066714
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background
Finished invoke:
  name: bg  status: 0  time: 0.014315
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 984.635245
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 54.817366
Invoking:
  centrimo -seqlen 467 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.137338
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.52969
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary MBSGGRATCGAACCSVKGAYCTYCHGRTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.537794
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary RBSSCTTWAMCMACTNRGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.481036
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary CCBRAAGTGATAACCAYTACACTATABSAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.315467
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary AAAARWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.568695
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.429412
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary GCCWTAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.264947
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary CGCTDCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.295742
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary DTCTTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.499255
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background -primary CCATCGTK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.226377
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif MBSGGRATCGAACCSVKGAYCTYCHGRTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.352631
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif RBSSCTTWAMCMACTNRGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.347918
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif CCBRAAGTGATAACCAYTACACTATABSAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.355783
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif AAAARWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.2208
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.22331
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif GCCWTAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.242629
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif CGCTDCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.237483
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif DTCTTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.222234
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/background --motif CCATCGTK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/BY4742--AFT1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.242663
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.153372
Done