Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.021284
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058803
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.077351
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.014082
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.064503
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background
Finished invoke:
  name: bg  status: 0  time: 0.016671
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 998.055952
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 51.876715
Invoking:
  centrimo -seqlen 748 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.132739
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.481943
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary MBSGGRRTCGAACCSVKGAYCTYHHGRTTR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.592744
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary GRDSSCBYWAMCVACTRSGCCAHRNRVSCW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.611747
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary GAAAARAAAAAAAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.573526
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary TACCACYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.276905
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary GCCTTAMC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.307611
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary RGAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.641963
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary GMTACCGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.281112
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary AGATCGKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.284158
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background -primary CTGGGGW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.278133
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif MBSGGRRTCGAACCSVKGAYCTYHHGRTTR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.449035
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif GRDSSCBYWAMCVACTRSGCCAHRNRVSCW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.450337
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif GAAAARAAAAAAAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.444494
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif TACCACYA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.323465
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif GCCTTAMC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.322362
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif RGAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.300684
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif GMTACCGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.328645
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif AGATCGKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.324367
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/background --motif CTGGGGW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/BY4741--SFL1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.30947
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.155223
Done