Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.051543
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.077964
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.078868
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013537
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.063496
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background
Finished invoke:
  name: bg  status: 0  time: 0.014831
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 963.862983
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 51.991868
Invoking:
  centrimo -seqlen 426 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.160382
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.353341
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary RRGRTCMBSGGTTCGATYCCSVKHGD /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.678578
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary SSYTYWAMCMACTRVRCYAHV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.756949
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary AAARWAAAAAAAARAAWRMVA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.557982
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary ACCAACTK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.300485
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.416316
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary GYGGTCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.253084
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.298701
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary AMGTTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.263401
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary ATTAASAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.283173
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary CAGAYGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.291337
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background -primary CYATGGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.312471
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif RRGRTCMBSGGTTCGATYCCSVKHGD /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.338011
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif SSYTYWAMCMACTRVRCYAHV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.339189
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif AAARWAAAAAAAARAAWRMVA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.368111
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif ACCAACTK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.22767
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.223067
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif GYGGTCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.23164
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.229774
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif AMGTTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.225518
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif ATTAASAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.225951
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif CAGAYGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.2164
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/background --motif CYATGGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/BY4741--CUP9.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.228975
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--CUP9/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.185753
Done