Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.018949
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058129
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.075188
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.015674
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.066443
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background
Finished invoke:
  name: bg  status: 0  time: 0.015515
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 772.416525
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 79.931919
Invoking:
  centrimo -seqlen 484 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.15768
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.422249
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary TCRKRRGRTCMBSGGTTCGAYYCCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.353084
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary AGSBYNNDTGGYBYAGTKGKTARMGCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.324388
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary WTWTBYTTGTTTAYHTTTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.526569
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary AGAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.562379
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary GGTADC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.426198
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary AACCAAYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.225313
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary ACCWCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.414103
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary CTTCMA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.483315
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary CAMCAAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.295776
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary CTCTAGM /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.224291
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background -primary CACCASC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.27928
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif TCRKRRGRTCMBSGGTTCGAYYCCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.320078
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif AGSBYNNDTGGYBYAGTKGKTARMGCS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.328582
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif WTWTBYTTGTTTAYHTTTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.317454
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif AGAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.212538
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif GGTADC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.211569
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif AACCAAYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.234939
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif ACCWCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.212237
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif CTTCMA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.212171
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif CAMCAAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.225987
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif CTCTAGM /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.241115
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/background --motif CACCASC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/RM11-1A--FKH1.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.232824
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--FKH1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.149377
Done