Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.019547
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.059368
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.077349
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013316
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.064423
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background
Finished invoke:
  name: bg  status: 0  time: 0.01605
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 989.962903
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 23.743242
Invoking:
  centrimo -seqlen 443 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.12722
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.29113
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background -primary SGGRATCGAACCCVGGAYCYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.419043
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background -primary CGCKYTACCVACTGGGCCAMV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.368617
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background -primary CAGAYTTRARATCTGTTGGRCKKTKSYCSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.29047
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background -primary AAAAAWAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.333215
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background -primary AGTGGTH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.280712
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background -primary SCCAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.267791
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background --motif SGGRATCGAACCCVGGAYCYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.369999
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background --motif CGCKYTACCVACTGGGCCAMV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.365431
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background --motif CAGAYTTRARATCTGTTGGRCKKTKSYCSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.380119
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background --motif AAAAAWAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.285462
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background --motif AGTGGTH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.257625
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/background --motif SCCAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/RM11-1A--MSS11.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.247013
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--MSS11/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.143086
Done