Invoking:
  fasta-get-markov -nostatus -m 1 < Dynamic_Male-biased_Output/Dynamic_Male-biased.fa 1> Dynamic_Male-biased_Output/background
Finished invoke:
  name: bg  status: 0  time: 0.035447
Invoking:
  getsize Dynamic_Male-biased_Output/Dynamic_Male-biased.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.027899
Invoking:
  fasta-most -min 50 < Dynamic_Male-biased_Output/Dynamic_Male-biased.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.08601
Invoking:
  fasta-center -len 100 < Dynamic_Male-biased_Output/Dynamic_Male-biased.fa 1> Dynamic_Male-biased_Output/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.116642
Invoking:
  fasta-dinucleotide-shuffle -f Dynamic_Male-biased_Output/seqs-centered -t -dinuc 1> Dynamic_Male-biased_Output/seqs-shuffled
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.745802
Invoking:
  fasta-subsample Dynamic_Male-biased_Output/seqs-centered 600 -rest Dynamic_Male-biased_Output/seqs-discarded 1> Dynamic_Male-biased_Output/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.074898
Invoking:
  meme Dynamic_Male-biased_Output/seqs-sampled -oc Dynamic_Male-biased_Output/meme_out -dna -mod anr -nmotifs 3 -minw 6 -maxw 30 -bfile Dynamic_Male-biased_Output/background -p 16 -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 99.866568
Invoking:
  dreme -v 1 -oc Dynamic_Male-biased_Output/dreme_out -p Dynamic_Male-biased_Output/seqs-centered -n Dynamic_Male-biased_Output/seqs-shuffled -png
Finished invoke:
  name: dreme  status: 0  time: 41.850745
Invoking:
  centrimo -seqlen 500 -verbosity 1 -oc Dynamic_Male-biased_Output/centrimo_out -bgfile Dynamic_Male-biased_Output/background Dynamic_Male-biased_Output/Dynamic_Male-biased.fa Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: centrimo  status: 0  time: 10.027541
Invoking:
  tomtom -verbosity 1 -oc Dynamic_Male-biased_Output/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile Dynamic_Male-biased_Output/background Dynamic_Male-biased_Output/meme_out/meme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 5.240683
Invoking:
  tomtom -verbosity 1 -oc Dynamic_Male-biased_Output/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile Dynamic_Male-biased_Output/background Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: dreme_tomtom  status: 0  time: 1.616241
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 Dynamic_Male-biased_Output/combined.meme Dynamic_Male-biased_Output/combined.meme 1> Dynamic_Male-biased_Output/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.585873
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_1 -bgfile Dynamic_Male-biased_Output/background -primary 3 Dynamic_Male-biased_Output/Dynamic_Male-biased.fa Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo1  status: 0  time: 9.531084
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_2 -bgfile Dynamic_Male-biased_Output/background -primary 1 Dynamic_Male-biased_Output/Dynamic_Male-biased.fa Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo2  status: 0  time: 6.59222
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_3 -bgfile Dynamic_Male-biased_Output/background -primary RATCAATA Dynamic_Male-biased_Output/Dynamic_Male-biased.fa Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo3  status: 0  time: 4.33706
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_4 -bgfile Dynamic_Male-biased_Output/background -primary CSTGSC Dynamic_Male-biased_Output/Dynamic_Male-biased.fa Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo4  status: 0  time: 10.350582
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_5 -bgfile Dynamic_Male-biased_Output/background -primary ACARAYA Dynamic_Male-biased_Output/Dynamic_Male-biased.fa Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo5  status: 0  time: 8.255807
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_6 -bgfile Dynamic_Male-biased_Output/background -primary MA0466.1 Dynamic_Male-biased_Output/Dynamic_Male-biased.fa ./JASPAR_CORE_2014_vertebrates.meme Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo6  status: 0  time: 9.212843
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_7 -bgfile Dynamic_Male-biased_Output/background -primary CTCTGH Dynamic_Male-biased_Output/Dynamic_Male-biased.fa Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo7  status: 0  time: 15.656236
Invoking:
  spamo -verbosity 1 -oc Dynamic_Male-biased_Output/spamo_out_8 -bgfile Dynamic_Male-biased_Output/background -primary MA0114.2 Dynamic_Male-biased_Output/Dynamic_Male-biased.fa ./JASPAR_CORE_2014_vertebrates.meme Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme
Finished invoke:
  name: spamo8  status: 0  time: 13.25198
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_1 --bgfile Dynamic_Male-biased_Output/background --motif 3 Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.434584
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_2 --bgfile Dynamic_Male-biased_Output/background --motif 1 Dynamic_Male-biased_Output/meme_out/meme.xml Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.809932
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_3 --bgfile Dynamic_Male-biased_Output/background --motif RATCAATA Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.17103
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_4 --bgfile Dynamic_Male-biased_Output/background --motif CSTGSC Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.134038
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_5 --bgfile Dynamic_Male-biased_Output/background --motif ACARAYA Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.184757
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_6 --bgfile Dynamic_Male-biased_Output/background --motif MA0466.1 ./JASPAR_CORE_2014_vertebrates.meme Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.230704
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_7 --bgfile Dynamic_Male-biased_Output/background --motif CTCTGH Dynamic_Male-biased_Output/dreme_out/dreme.xml Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.13286
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc Dynamic_Male-biased_Output/fimo_out_8 --bgfile Dynamic_Male-biased_Output/background --motif MA0114.2 ./JASPAR_CORE_2014_vertebrates.meme Dynamic_Male-biased_Output/Dynamic_Male-biased.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.266593
Writing output
Done