Invoking:
  getsize memechip_example_output_files/Klf1.fna 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.047092
Invoking:
  fasta-most -min 50 < memechip_example_output_files/Klf1.fna 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.096994
Invoking:
  fasta-center -dna -len 100 < memechip_example_output_files/Klf1.fna 1> memechip_example_output_files/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.123679
Invoking:
  fasta-shuffle-letters memechip_example_output_files/seqs-centered memechip_example_output_files/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.044569
Invoking:
  fasta-subsample memechip_example_output_files/seqs-centered 600 -rest memechip_example_output_files/seqs-discarded -seed 1 1> memechip_example_output_files/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.115345
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 memechip_example_output_files/Klf1.fna memechip_example_output_files/background
Finished invoke:
  name: bg  status: 0  time: 0.027028
Invoking:
  meme memechip_example_output_files/seqs-sampled -oc memechip_example_output_files/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile memechip_example_output_files/background -dna -p 6 -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 507.794987
Invoking:
  dreme -v 1 -oc memechip_example_output_files/dreme_out -png -dna -p memechip_example_output_files/seqs-centered -n memechip_example_output_files/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 42.365221
Invoking:
  centrimo -seqlen 500 -verbosity 1 -oc memechip_example_output_files/centrimo_out -bfile memechip_example_output_files/background memechip_example_output_files/Klf1.fna memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2014.meme
Finished invoke:
  name: centrimo  status: 0  time: 10.243691
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_2014.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 8.02692
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_2014.meme
Finished invoke:
  name: dreme_tomtom  status: 0  time: 0.71049
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: 1.136114
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_1 -bgfile memechip_example_output_files/background -primary 1 memechip_example_output_files/Klf1.fna 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_2014.meme
Finished invoke:
  name: spamo1  status: 0  time: 16.15403
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_2 -bgfile memechip_example_output_files/background -primary TTATCW memechip_example_output_files/Klf1.fna memechip_example_output_files/dreme_out/dreme.xml memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2014.meme
Finished invoke:
  name: spamo2  status: 0  time: 12.648643
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_3 -bgfile memechip_example_output_files/background -primary MA0545.1 memechip_example_output_files/Klf1.fna JASPAR_CORE_2014.meme memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2014.meme
Finished invoke:
  name: spamo3  status: 0  time: 5.612381
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_4 -bgfile memechip_example_output_files/background -primary MA0204.1 memechip_example_output_files/Klf1.fna JASPAR_CORE_2014.meme memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2014.meme
Finished invoke:
  name: spamo4  status: 0  time: 6.297089
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_5 -bgfile memechip_example_output_files/background -primary MA0531.1 memechip_example_output_files/Klf1.fna JASPAR_CORE_2014.meme memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2014.meme
Finished invoke:
  name: spamo5  status: 0  time: 4.709446
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/Klf1.fna
Finished invoke:
  name: fimo1  status: 0  time: 0.610631
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_2 --bgfile memechip_example_output_files/background --motif TTATCW memechip_example_output_files/dreme_out/dreme.xml memechip_example_output_files/Klf1.fna
Finished invoke:
  name: fimo2  status: 0  time: 0.436289
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_3 --bgfile memechip_example_output_files/background --motif MA0545.1 JASPAR_CORE_2014.meme memechip_example_output_files/Klf1.fna
Finished invoke:
  name: fimo3  status: 0  time: 0.701965
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_4 --bgfile memechip_example_output_files/background --motif MA0204.1 JASPAR_CORE_2014.meme memechip_example_output_files/Klf1.fna
Finished invoke:
  name: fimo4  status: 0  time: 0.693154
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_5 --bgfile memechip_example_output_files/background --motif MA0531.1 JASPAR_CORE_2014.meme memechip_example_output_files/Klf1.fna
Finished invoke:
  name: fimo5  status: 0  time: 0.70591
Writing output
Done
