Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.014056
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056156
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.07017
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012074
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background
Finished invoke:
  name: bg  status: 0  time: 0.012767
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1285.814383
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 24.733939
Invoking:
  centrimo -seqlen 461 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.123909
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.249266
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -primary DMSSGGRATCGAACCSSGGAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.37773
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -primary SSCTYWAMCCACTRRRCYAHVVVV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.383957
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -primary CACCCAYRCACCACACCCASA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.230545
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -primary CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.22444
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -primary AAAAARAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.282546
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -primary GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.196626
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background -primary ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.188237
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background --motif DMSSGGRATCGAACCSSGGAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.253911
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background --motif SSCTYWAMCCACTRRRCYAHVVVV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.247977
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background --motif CACCCAYRCACCACACCCASA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.257774
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background --motif CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.162702
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background --motif AAAAARAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.169658
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background --motif GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.170037
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/background --motif ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/RM11-1A--ARR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.169143
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--ARR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.142108
Done