Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.127251
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.075816
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.099189
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.03532
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.080122
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background
Finished invoke:
  name: bg  status: 0  time: 0.037255
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 984.570943
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 54.913883
Invoking:
  centrimo -seqlen 480 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.180217
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.26971
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary GRTCMBSGGTTCGATYCCSSK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.693444
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary GSBCNNKTGGYBYAGTGGKWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.7273
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary RARAAAAAAARAAWAWDRAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.580795
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.343128
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.314861
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary CTTGRCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.373316
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.45973
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary AAGGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.389375
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary CTGGGGWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.341181
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background -primary CACGGYG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.274527
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif GRTCMBSGGTTCGATYCCSSK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.452336
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif GSBCNNKTGGYBYAGTGGKWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.474259
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif RARAAAAAAARAAWAWDRAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.507671
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.34502
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.364844
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif CTTGRCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.570543
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.32354
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif AAGGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.299569
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif CTGGGGWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.332916
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/background --motif CACGGYG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/BY4741--MOT3.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.321747
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.231069
Done