Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.14171
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.073176
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.104649
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.035718
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.087221
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background
Finished invoke:
  name: bg  status: 0  time: 0.037041
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1005.587284
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 45.0719
Invoking:
  centrimo -seqlen 1416 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.224806
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.372987
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary RGRTYVSSGGTTCRATTCCSSBHBGGGGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.525497
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary WGSBBMNKTGGCBNAGTKGKWWARGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.531238
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary TTTTTTTTTTTTTYTYCWTYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.67417
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary SAAGAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.673798
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary YGGTAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.709663
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary CTTGRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.620974
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary AACCACT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.346493
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background -primary GCCGCY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.45222
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif RGRTYVSSGGTTCRATTCCSSBHBGGGGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.802499
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif WGSBBMNKTGGCBNAGTKGKWWARGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.608459
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif TTTTTTTTTTTTTYTYCWTYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.633311
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif SAAGAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.445259
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif YGGTAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.436507
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif CTTGRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.431323
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif AACCACT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.651202
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/background --motif GCCGCY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/RM11-1A--RPD3.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.46492
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.226102
Done