Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.015928
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.055572
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.073134
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.012116
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.062128
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background
Finished invoke:
  name: bg  status: 0  time: 0.013008
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 976.172006
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 39.68217
Invoking:
  centrimo -seqlen 565 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.139217
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.235058
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary AGRTCMBSGGTTCGATYCCSV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.571402
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary WGSBYNYDTGGCBYAGTGGK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.636716
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary TAAGGCRYCDSVCTWDYAAKS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.548174
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary ARAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.441618
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.374806
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary CTYACGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.241801
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary CGTGYTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.222742
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background -primary AGARGTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.244405
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif AGRTCMBSGGTTCGATYCCSV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.306081
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif WGSBYNYDTGGCBYAGTGGK /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.304351
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif TAAGGCRYCDSVCTWDYAAKS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.301536
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif ARAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.185201
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.185864
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif CTYACGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.218279
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif CGTGYTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.214223
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/background --motif AGARGTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/BY4742--SMP1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.198713
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.140935
Done