Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.100549
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.068874
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.087079
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.02667
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.079431
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background
Finished invoke:
  name: bg  status: 0  time: 0.026241
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 952.018979
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 70.290748
Invoking:
  centrimo -seqlen 350 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.458152
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.606524
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary SNRDCSCYYWAMCVACTVSGCCAMVVRVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.389363
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary TNGTAAYSDDRAGRTCMKSGGTTCGANYCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.373107
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary RDRRTGTAYGGRTGT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.354716
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary BTAAGGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.236014
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary GCKCTMCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.247894
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary AARAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.253153
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary CCWTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.239974
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary CATYACGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.212155
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary ACTGAGCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.426326
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background -primary CYACACTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.225387
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif SNRDCSCYYWAMCVACTVSGCCAMVVRVSC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.267213
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif TNGTAAYSDDRAGRTCMKSGGTTCGANYCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.251655
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif RDRRTGTAYGGRTGT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.24566
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif BTAAGGCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.143372
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif GCKCTMCC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.166572
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif AARAAAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.144383
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif CCWTAACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.358412
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif CATYACGC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.165987
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif ACTGAGCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.139013
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/background --motif CYACACTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/BY4741--HIR1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.157187
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.170683
Done