Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.015594
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.057152
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.072941
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012644
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background
Finished invoke:
  name: bg  status: 0  time: 0.01262
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 877.793524
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 33.29472
Invoking:
  centrimo -seqlen 449 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.154479
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.646951
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary GGTTCGATYCYSSBHKNGRKCRTTTTTTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.418098
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary BTBDTRGYBYAGTKGKTARAGSSNYCGVYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.390934
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary ATTWSRAGTCSRAMGCKCTACCAYTRMGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.295418
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.29908
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.24455
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary GTGATAGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.201043
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary CTTAAYCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.223955
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary CACGRTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.224106
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background -primary GSGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.247303
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif GGTTCGATYCYSSBHKNGRKCRTTTTTTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.28921
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif BTBDTRGYBYAGTKGKTARAGSSNYCGVYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.285249
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif ATTWSRAGTCSRAMGCKCTACCAYTRMGCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.280975
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif AAAAADAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.2002
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif CCCATDC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.18095
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif GTGATAGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.211315
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif CTTAAYCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.194717
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif CACGRTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.179754
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/background --motif GSGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/RM11-1A--SRB8.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.181956
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.15621
Done