Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.033993
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.059744
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.082326
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.023439
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background
Finished invoke:
  name: bg  status: 0  time: 0.018925
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 940.471384
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 50.414665
Invoking:
  centrimo -seqlen 444 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.216066
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.509384
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary WGSBBNBDTRGYBYAGTGGKTARAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.681716
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary CMBSGGTTCGATYCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.659194
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary GKTARSGCGYCWSACTHNTAATSWGRAGRT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.533432
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary ARAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.513227
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.317261
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary CACTTKCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.23558
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary AGARTCAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.245252
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary GGTCTM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.37738
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary ACGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.300692
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary CCGKACA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.293524
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background -primary GTCTGRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.250808
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif WGSBBNBDTRGYBYAGTGGKTARAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.308243
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif CMBSGGTTCGATYCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.353275
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif GKTARSGCGYCWSACTHNTAATSWGRAGRT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.338011
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif ARAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.181676
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.222631
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif CACTTKCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.234285
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif AGARTCAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.249391
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif GGTCTM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.200743
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif ACGKTGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.228424
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif CCGKACA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.221287
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/background --motif GTCTGRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/BY4741--RIM101.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.247923
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--RIM101/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.196089
Done