Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.177339
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.06963
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.093721
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.031296
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.080368
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background
Finished invoke:
  name: bg  status: 0  time: 0.035086
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1007.76081
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 34.604777
Invoking:
  centrimo -seqlen 545 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.182742
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.376758
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background -primary DSSSGGRATCGAACCCSSGACCTYMNGRTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.540963
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background -primary TGGCCNAGTBGGTWRWGSSNYMSRCTTDW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.464784
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background -primary RAAAAAADAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.444608
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background -primary TAGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.286554
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background -primary CGSTTGTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.235799
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background -primary RCGGGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.256361
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background --motif DSSSGGRATCGAACCCSSGACCTYMNGRTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.527931
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background --motif TGGCCNAGTBGGTWRWGSSNYMSRCTTDW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.741159
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background --motif RAAAAAADAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.513111
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background --motif TAGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.405647
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background --motif CGSTTGTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.414556
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/background --motif RCGGGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.382585
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.163532
Done