Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.01988
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.05892
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.076225
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013412
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.065751
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background
Finished invoke:
  name: bg  status: 0  time: 0.016047
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 990.721789
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 29.720941
Invoking:
  centrimo -seqlen 566 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.130612
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.427741
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background -primary AAAAAAAAYGMYCMSDMBSGGRDTCGAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.443703
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background -primary CGNNSSCTTWWMCCACTRRRCYAHVVVVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.473757
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background -primary CYHMACMCVCASAMCRYMCCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.262783
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background -primary AAGADA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.387237
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background -primary AAAAATR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.437761
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background -primary CGGTADC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.239806
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background --motif AAAAAAAAYGMYCMSDMBSGGRDTCGAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.408699
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background --motif CGNNSSCTTWWMCCACTRRRCYAHVVVVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.409213
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background --motif CYHMACMCVCASAMCRYMCCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.404409
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background --motif AAGADA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.275184
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background --motif AAAAATR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.268024
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/background --motif CGGTADC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/RM11-1A--STE12.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.281106
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--STE12/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.187888
Done