Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.063852
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058151
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.309299
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.050191
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.086521
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background
Finished invoke:
  name: bg  status: 0  time: 0.024789
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 929.896121
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 58.170104
Invoking:
  centrimo -seqlen 440 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.235338
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.491607
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary WGSBYNYDTGGCSBAGTGGKTWRRGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.436685
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary KRRGRTCVBSGGTTCGATYCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.404874
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary CMCWCACMCACACAMMCAYACCACACCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.265302
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.23599
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary AAGAVAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.285234
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary GCGCTWCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.232998
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.217316
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary CACCGTGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.213338
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.213112
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background -primary AGTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.209293
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif WGSBYNYDTGGCSBAGTGGKTWRRGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.272088
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif KRRGRTCVBSGGTTCGATYCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.246342
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif CMCWCACMCACACAMMCAYACCACACCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.286203
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.164163
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif AAGAVAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.162008
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif GCGCTWCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.172973
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.160815
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif CACCGTGS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.152902
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.169938
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/background --motif AGTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/BY4741--ARR1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.167235
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.280771
Done