Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.029504
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.067575
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.084052
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012642
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background
Finished invoke:
  name: bg  status: 0  time: 0.039659
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 868.513297
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 29.822113
Invoking:
  centrimo -seqlen 689 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.159721
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.326244
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary RAGRTCVBSGGTTCGANYCCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.434843
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary TGGYYYAGTBGKTWRAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.404391
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary TAGAAGTTCTCCTCGAGGATATAGGAATC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.251637
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary CCWTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.23047
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary AAAAATAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.301046
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.201268
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary GCGCAAK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.196217
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background -primary ACCATCM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.212008
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif RAGRTCVBSGGTTCGANYCCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.343413
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif TGGYYYAGTBGKTWRAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.321695
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif TAGAAGTTCTCCTCGAGGATATAGGAATC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.341264
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif CCWTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.234029
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif AAAAATAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.223173
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.241105
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif GCGCAAK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.238601
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/background --motif ACCATCM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/BY4741--SWI1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.233717
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SWI1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.172476
Done