Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.01389
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.0574
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.070582
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.01239
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.064912
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background
Finished invoke:
  name: bg  status: 0  time: 0.011846
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 808.551769
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 56.056426
Invoking:
  centrimo -seqlen 476 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.159224
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.390672
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary YKTGGCCBAGTKGKWWRRGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.27042
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary TCGAACCSVKGAYCTYMNGAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.266782
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary RSSKVAHGTGATARCCRYTACACTATADSR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.238618
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary ACCRACT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.195912
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary AGAARM /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.285886
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary AGAGCGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.152143
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary GTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.188042
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary GCMACAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.171667
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background -primary ACTGGGR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.162596
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif YKTGGCCBAGTKGKWWRRGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.24558
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif TCGAACCSVKGAYCTYMNGAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.24747
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif RSSKVAHGTGATARCCRYTACACTATADSR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.250457
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif ACCRACT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.161893
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif AGAARM /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.145167
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif AGAGCGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.164217
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif GTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.159427
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif GCMACAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.183143
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/background --motif ACTGGGR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/RM11-1A--SFL1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.162057
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SFL1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.161654
Done