Invoking:
  fasta-get-markov -nostatus -m 1 < memechip_example_output_files/sample-dna-Klf1.fa 1> memechip_example_output_files/background
Finished invoke:
  name: bg  status: 0  time: 0.015515
Invoking:
  getsize memechip_example_output_files/sample-dna-Klf1.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.019767
Invoking:
  fasta-most -min 50 < memechip_example_output_files/sample-dna-Klf1.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.03889
Invoking:
  fasta-center -len 100 < memechip_example_output_files/sample-dna-Klf1.fa 1> memechip_example_output_files/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.026273
Invoking:
  fasta-dinucleotide-shuffle -f memechip_example_output_files/seqs-centered -t -dinuc 1> memechip_example_output_files/seqs-shuffled
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.666054
Invoking:
  fasta-subsample memechip_example_output_files/seqs-centered 600 -rest memechip_example_output_files/seqs-discarded 1> memechip_example_output_files/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.043721
Invoking:
  meme memechip_example_output_files/seqs-sampled -oc memechip_example_output_files/meme_out -dna -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile memechip_example_output_files/background -p 6 -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 504.485464
Invoking:
  dreme -v 1 -oc memechip_example_output_files/dreme_out -p memechip_example_output_files/seqs-centered -n memechip_example_output_files/seqs-shuffled -png
Finished invoke:
  name: dreme  status: 0  time: 17.122759
Invoking:
  centrimo -seqlen 500 -verbosity 1 -oc memechip_example_output_files/centrimo_out -bgfile memechip_example_output_files/background memechip_example_output_files/sample-dna-Klf1.fa memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: centrimo  status: 0  time: 14.716704
Invoking:
  tomtom -verbosity 1 -oc memechip_example_output_files/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile memechip_example_output_files/background memechip_example_output_files/meme_out/meme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 18.602552
Invoking:
  tomtom -verbosity 1 -oc memechip_example_output_files/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile memechip_example_output_files/background memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: dreme_tomtom  status: 0  time: 0.720525
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 memechip_example_output_files/combined.meme memechip_example_output_files/combined.meme 1> memechip_example_output_files/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 2.076766
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_1 -bgfile memechip_example_output_files/background -primary 1 memechip_example_output_files/sample-dna-Klf1.fa memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: spamo1  status: 0  time: 14.137113
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_2 -bgfile memechip_example_output_files/background -primary 2 memechip_example_output_files/sample-dna-Klf1.fa memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: spamo2  status: 0  time: 11.482534
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_3 -bgfile memechip_example_output_files/background -primary MA0450.1 memechip_example_output_files/sample-dna-Klf1.fa JASPAR_CORE_2009.meme memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: spamo3  status: 0  time: 6.024557
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_4 -bgfile memechip_example_output_files/background -primary MA0036.1 memechip_example_output_files/sample-dna-Klf1.fa JASPAR_CORE_2009.meme memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: spamo4  status: 0  time: 0.575319
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_5 -bgfile memechip_example_output_files/background -primary MA0204.1 memechip_example_output_files/sample-dna-Klf1.fa JASPAR_CORE_2009.meme memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme
Finished invoke:
  name: spamo5  status: 0  time: 6.486124
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_1 --bgfile memechip_example_output_files/background --motif 1 memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/sample-dna-Klf1.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.461931
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_2 --bgfile memechip_example_output_files/background --motif 2 memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/sample-dna-Klf1.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.312282
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_3 --bgfile memechip_example_output_files/background --motif MA0450.1 JASPAR_CORE_2009.meme memechip_example_output_files/sample-dna-Klf1.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.410452
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_4 --bgfile memechip_example_output_files/background --motif MA0036.1 JASPAR_CORE_2009.meme memechip_example_output_files/sample-dna-Klf1.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.356734
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_5 --bgfile memechip_example_output_files/background --motif MA0204.1 JASPAR_CORE_2009.meme memechip_example_output_files/sample-dna-Klf1.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.367655
Writing output
Done
