Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.014557
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056275
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.071985
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012203
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background
Finished invoke:
  name: bg  status: 0  time: 0.012585
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 620.508684
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 29.273055
Invoking:
  centrimo -seqlen 512 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.125272
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.486518
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary RGRTCVSSGGTTCGAWYCYSSBHKNGRKCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.478028
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary VSCYTWAMCCACTVRGCCAM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.453014
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary THWMATCCGWKATAGTKTAAYGGYYAKMAY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.286598
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary ARAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.351022
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.220396
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary CGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.290605
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary GAAGAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.295473
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background -primary CCGTSG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.274234
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif RGRTCVSSGGTTCGAWYCYSSBHKNGRKCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.263943
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif VSCYTWAMCCACTVRGCCAM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.249012
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif THWMATCCGWKATAGTKTAAYGGYYAKMAY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.260636
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif ARAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.150566
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.164257
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif CGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.167134
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif GAAGAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.166935
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/background --motif CCGTSG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/YJM789--HIR1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.167057
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.148984
Done