Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.012356
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.056102
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.069941
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.011158
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background
Finished invoke:
  name: bg  status: 0  time: 0.010547
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-centered -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 593.96352
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 22.940819
Invoking:
  centrimo -seqlen 565 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.158835
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.399543
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background -primary MCSGGRMTCGAACCSGBGAYCTYMHGVTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.416195
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background -primary SGNNSSCTYWAMCVACTNGGCCAMNNRVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.373093
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background -primary TRNGRTGYAYGGRTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.336538
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background -primary CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.204822
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background -primary AARAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.316269
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background --motif MCSGGRMTCGAACCSGBGAYCTYMHGVTT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.251974
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background --motif SGNNSSCTYWAMCVACTNGGCCAMNNRVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.264552
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background --motif TRNGRTGYAYGGRTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.246337
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background --motif CGCCTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.162831
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/background --motif AARAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/YJM789--HAA1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.148816
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.151597
Done