Invoking:
  getsize memechip_out/orig.idr.cut-not-seq.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.009389
Invoking:
  fasta-most -min 50 < memechip_out/orig.idr.cut-not-seq.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.046613
Invoking:
  fasta-center -dna -len 100 < memechip_out/orig.idr.cut-not-seq.fa 1> memechip_out/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.054891
Invoking:
  fasta-shuffle-letters memechip_out/seqs-centered memechip_out/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.008254
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 memechip_out/orig.idr.cut-not-seq.fa memechip_out/background
Finished invoke:
  name: bg  status: 0  time: 0.006001
Invoking:
  meme memechip_out/seqs-centered -oc memechip_out/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile memechip_out/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 337.830583
Invoking:
  dreme -v 1 -oc memechip_out/dreme_out -png -dna -p memechip_out/seqs-centered -n memechip_out/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 17.304366
Invoking:
  centrimo -seqlen 201 -verbosity 1 -oc memechip_out/centrimo_out -bfile memechip_out/background memechip_out/orig.idr.cut-not-seq.fa memechip_out/meme_out/meme.xml memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.135891
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 memechip_out/combined.meme memechip_out/combined.meme 1> memechip_out/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.097516
Invoking:
  spamo -verbosity 1 -oc memechip_out/spamo_out_1 -bgfile memechip_out/background -primary CTGTCCRTGGTGCTGAA memechip_out/orig.idr.cut-not-seq.fa memechip_out/meme_out/meme.xml memechip_out/meme_out/meme.xml memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.256491
Invoking:
  spamo -verbosity 1 -oc memechip_out/spamo_out_2 -bgfile memechip_out/background -primary BWMATTWGCATAWHAWWWR memechip_out/orig.idr.cut-not-seq.fa memechip_out/meme_out/meme.xml memechip_out/meme_out/meme.xml memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.291987
Invoking:
  spamo -verbosity 1 -oc memechip_out/spamo_out_3 -bgfile memechip_out/background -primary GGACAGCKCCM memechip_out/orig.idr.cut-not-seq.fa memechip_out/meme_out/meme.xml memechip_out/meme_out/meme.xml memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.210626
Invoking:
  spamo -verbosity 1 -oc memechip_out/spamo_out_4 -bgfile memechip_out/background -primary GMCAGKA memechip_out/orig.idr.cut-not-seq.fa memechip_out/dreme_out/dreme.xml memechip_out/meme_out/meme.xml memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.145545
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_out/fimo_out_1 --bgfile memechip_out/background --motif CTGTCCRTGGTGCTGAA memechip_out/meme_out/meme.xml memechip_out/orig.idr.cut-not-seq.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.186058
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_out/fimo_out_2 --bgfile memechip_out/background --motif BWMATTWGCATAWHAWWWR memechip_out/meme_out/meme.xml memechip_out/orig.idr.cut-not-seq.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.217017
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_out/fimo_out_3 --bgfile memechip_out/background --motif GGACAGCKCCM memechip_out/meme_out/meme.xml memechip_out/orig.idr.cut-not-seq.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.169866
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc memechip_out/fimo_out_4 --bgfile memechip_out/background --motif GMCAGKA memechip_out/dreme_out/dreme.xml memechip_out/orig.idr.cut-not-seq.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.072013
Writing output
Invoking:
  meme-chip_html_to_tsv memechip_out/meme-chip.html memechip_out/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.125651
Done