Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.017611
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058569
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.073145
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012425
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background
Finished invoke:
  name: bg  status: 0  time: 0.012063
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 827.033215
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 43.205325
Invoking:
  centrimo -seqlen 499 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.13224
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.386644
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary AGRTCVBSGGTTCGATYCCSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.452681
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary RNSSCTYWACCAACTKGGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.405247
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary KCGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.23085
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.34147
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.222585
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary GCKCTAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.202207
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.244574
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.232931
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary KAGTGGTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.210776
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary ATCKTGAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.196492
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background -primary CATCCGTR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.178867
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif AGRTCVBSGGTTCGATYCCSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.265149
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif RNSSCTYWACCAACTKGGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.270895
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif KCGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.177345
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.179691
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.176535
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif GCKCTAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.172805
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.175045
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.178538
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif KAGTGGTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.177069
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif ATCKTGAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.17496
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/background --motif CATCCGTR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/BY4741--CUP2.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.18034
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP2/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.152402
Done