Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.034954
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058261
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.079831
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013506
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.063589
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background
Finished invoke:
  name: bg  status: 0  time: 0.016522
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 978.226758
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 48.134715
Invoking:
  centrimo -seqlen 560 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.146321
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.346931
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background -primary RAGRTCVBSGGTTCGAYYCCSVBHGDGRSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.759229
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background -primary TAMCCACTRSRCCAMRNRVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.704343
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background -primary TTTTYTTTTTYTTTY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.625605
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background -primary GCCWTAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.307806
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background -primary GCGCYAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.348057
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background -primary CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.537549
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background --motif RAGRTCVBSGGTTCGAYYCCSVBHGDGRSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.389824
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background --motif TAMCCACTRSRCCAMRNRVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.376454
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background --motif TTTTYTTTTTYTTTY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.38823
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background --motif GCCWTAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.262893
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background --motif GCGCYAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.25137
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/background --motif CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/BY4742--SWI1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.239552
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.143054
Done