Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.073106
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.063668
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.077356
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.028076
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background
Finished invoke:
  name: bg  status: 0  time: 0.016649
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 912.163318
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 23.307322
Invoking:
  centrimo -seqlen 532 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.353496
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.389577
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background -primary RRGRTCMBSGGTTCGAYYCCSVKHKDGRG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.57769
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background -primary SSCYYTWMCCACTRVRCCAH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.395058
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background -primary AAAAAKAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.281993
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background -primary DCGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.203612
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background -primary RCGGGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.190733
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background -primary CGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.189467
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background --motif RRGRTCMBSGGTTCGAYYCCSVKHKDGRG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.340961
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background --motif SSCYYTWMCCACTRVRCCAH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.298101
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background --motif AAAAAKAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.228976
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background --motif DCGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.222817
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background --motif RCGGGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.220779
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/background --motif CGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/RM11-1A--AFT1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.207575
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.15523
Done