Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.016337
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.059234
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.076686
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.014488
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.067097
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background
Finished invoke:
  name: bg  status: 0  time: 0.012832
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 875.994043
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 65.774921
Invoking:
  centrimo -seqlen 524 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.167928
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.406451
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary AGSBYNYDTGGCSYAGTKGKWWR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.366129
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary RAGRTCMKGGGTTCGANYCCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.310328
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary WNYWTTTTTTTWHTTTTTTTTTTTNTTTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.364451
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary CCHTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.199416
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary RAGAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.360895
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary GCCAAGW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.217438
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary AGCKAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.163172
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary CGMTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.182803
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary ATATAYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.253734
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary AMGATGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.215594
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary ACCACTR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.19114
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/spamo_out_12 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background -primary CACGGYG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo12  status: 0  time: 0.185133
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif AGSBYNYDTGGCSYAGTKGKWWR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.254651
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif RAGRTCMKGGGTTCGANYCCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.250323
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif WNYWTTTTTTTWHTTTTTTTTTTTNTTTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.288415
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif CCHTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.170087
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif RAGAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.148486
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif GCCAAGW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.169182
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif AGCKAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.166082
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif CGMTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.167861
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif ATATAYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.152964
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif AMGATGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.178531
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif ACCACTR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.169904
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/background --motif CACGGYG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo12  status: 0  time: 0.167248
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.151729
Done