Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.022402
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.055964
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.072859
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.023509
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.069689
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background
Finished invoke:
  name: bg  status: 0  time: 0.01494
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 954.053601
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 79.771785
Invoking:
  centrimo -seqlen 456 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.218062
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.336713
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary SSCYTWAMCMACTBGGCCAMR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.500884
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary AGRTCMBSGGTTCGAYYCCSV /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.552931
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary YMWHWTWACAYCCRTACAYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.434227
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.305043
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.238842
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.275953
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary AARAAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.509386
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary GTGATAGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.240964
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary TAGCTCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.232341
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.363084
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary CCGTGSA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.245696
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/spamo_out_12 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background -primary AAGCGWGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml
Finished invoke:
  name: spamo12  status: 0  time: 0.216357
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif SSCYTWAMCMACTBGGCCAMR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.269656
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif AGRTCMBSGGTTCGAYYCCSV /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.235623
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif YMWHWTWACAYCCRTACAYY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.243423
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif CGCSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.146277
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif GCKCTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.150384
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.154612
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif AARAAAR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.137677
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif GTGATAGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.150698
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif TAGCTCR /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.151428
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif CRCCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.122004
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif CCGTGSA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.148445
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/background --motif AAGCGWGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/BY4741--SWR1.fa
Finished invoke:
  name: fimo12  status: 0  time: 0.150829
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWR1/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.180147
Done