Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.030829
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.060501
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.073107
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.015273
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.063756
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background
Finished invoke:
  name: bg  status: 0  time: 0.013953
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 953.388807
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 60.718172
Invoking:
  centrimo -seqlen 452 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.180718
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.678546
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary MBSGGRMTCGAACCSVBGAYC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.667637
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary GGCSVADTKGKTARSGCGYHWGACTNNWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.569135
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary ACCAYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.521992
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.613927
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary ACCRACT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.374369
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.408183
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary GTCTGRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.314718
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary DATGGCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.396899
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary CGCGGGSA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.354134
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary CCWACAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.29054
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background -primary AGARTCAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.273386
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif MBSGGRMTCGAACCSVBGAYC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.333801
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif GGCSVADTKGKTARSGCGYHWGACTNNWAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.349099
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif ACCAYT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.21292
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.201417
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif ACCRACT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.226197
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.228327
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif GTCTGRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.218002
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif DATGGCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.231521
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif CGCGGGSA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.234878
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif CCWACAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.22155
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/background --motif AGARTCAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/BY4742--MSS11.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.222126
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.154656
Done