Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.015833
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.057145
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.070351
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.01205
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background
Finished invoke:
  name: bg  status: 0  time: 0.013002
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 771.449063
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 24.401028
Invoking:
  centrimo -seqlen 575 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.127167
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.37581
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -primary GGTCVBSGGTTCGATYCCSSKHKDGRBCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.469852
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -primary AVARBCKNACGYKMTAVCCAYTRMRCTAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.335763
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -primary GGCCSAGTKGKTTAAGGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.295885
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -primary AARAARA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.338245
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -primary GATGWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.251827
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -primary RCGGGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.195247
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background -primary CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.210162
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background --motif GGTCVBSGGTTCGATYCCSSKHKDGRBCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.282842
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background --motif AVARBCKNACGYKMTAVCCAYTRMRCTAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.279756
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background --motif GGCCSAGTKGKTTAAGGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.267774
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background --motif AARAARA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.168632
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background --motif GATGWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.171748
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background --motif RCGGGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.185048
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/background --motif CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.184439
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YRR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.144143
Done