Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.017697
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.058338
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.074141
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.013384
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.064331
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background
Finished invoke:
  name: bg  status: 0  time: 0.013514
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 972.799109
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 49.857681
Invoking:
  centrimo -seqlen 548 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.14967
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.609871
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary VDRAGRTCMBSGGTTCGAKYCCSVKH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.495103
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary GCCWTAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.272833
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary ARAAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.395568
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary AACCACTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.248211
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.213112
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary AGACCRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.259094
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary AACTKGGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.232767
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary AGAYCGGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.207318
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary AGMAGAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.286571
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background -primary TCGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.270474
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif VDRAGRTCMBSGGTTCGAKYCCSVKH /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.329141
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif GCCWTAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.22476
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif ARAAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.24054
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif AACCACTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.223567
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.224515
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif AGACCRC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.220086
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif AACTKGGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.226848
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif AGAYCGGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.225104
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif AGMAGAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.219887
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/background --motif TCGSCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/BY4741--PHD1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.217091
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--PHD1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.150066
Done