Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.018354
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058571
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.074891
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.015295
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.068075
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background
Finished invoke:
  name: bg  status: 0  time: 0.013959
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 847.679015
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 79.610639
Invoking:
  centrimo -seqlen 524 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.166951
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.476792
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary SSCTYWAMCVACTVGGCCAMRNRVS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.297751
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary RAGGTYMKGGGTTCGABYCCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.265808
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary AAGARA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.362135
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary GCKKCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.221583
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary ATRGCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.294726
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary KCGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.174763
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.197915
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary CWGACGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.172663
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary KATATA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.276921
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background -primary GTTAGTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.153091
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif SSCTYWAMCVACTVGGCCAMRNRVS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.285745
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif RAGGTYMKGGGTTCGABYCCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.280415
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif AAGARA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.179505
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif GCKKCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.198797
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif ATRGCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.180597
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif KCGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.201382
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.197787
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif CWGACGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.196338
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif KATATA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.179809
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/background --motif GTTAGTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/BY4742--RPD3.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.198957
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPD3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.152421
Done