Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.030617
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056923
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.082094
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.023952
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background
Finished invoke:
  name: bg  status: 0  time: 0.027742
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 984.028953
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 23.988914
Invoking:
  centrimo -seqlen 509 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.227907
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.372211
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background -primary BSGGRWTCGAACCSVKGAYCTYMN /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.476685
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background -primary CRRWKGGKTAAGGCGYMDGACTNNWAATS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.365579
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background -primary GTGGYBTAGTGGKKARVGCSHHC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.413577
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background -primary AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.349869
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background -primary CAASAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.277294
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background -primary ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.246218
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background --motif BSGGRWTCGAACCSVKGAYCTYMN /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.316554
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background --motif CRRWKGGKTAAGGCGYMDGACTNNWAATS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.318185
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background --motif GTGGYBTAGTGGKKARVGCSHHC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.309584
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background --motif AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.22205
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background --motif CAASAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.210231
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.240557
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CIN5/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.211052
Done