Invoking:
  getsize cutnotseq_memechip_out/cut-not-seq.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.080697
Invoking:
  fasta-most -min 50 < cutnotseq_memechip_out/cut-not-seq.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.06528
Invoking:
  fasta-center -dna -len 100 < cutnotseq_memechip_out/cut-not-seq.fa 1> cutnotseq_memechip_out/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.08874
Invoking:
  fasta-shuffle-letters cutnotseq_memechip_out/seqs-centered cutnotseq_memechip_out/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.037394
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 cutnotseq_memechip_out/cut-not-seq.fa cutnotseq_memechip_out/background
Finished invoke:
  name: bg  status: 0  time: 0.033434
Invoking:
  meme cutnotseq_memechip_out/seqs-centered -oc cutnotseq_memechip_out/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile cutnotseq_memechip_out/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 460.35566
Invoking:
  dreme -v 1 -oc cutnotseq_memechip_out/dreme_out -png -dna -p cutnotseq_memechip_out/seqs-centered -n cutnotseq_memechip_out/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 15.880077
Invoking:
  centrimo -seqlen 576 -verbosity 1 -oc cutnotseq_memechip_out/centrimo_out -bfile cutnotseq_memechip_out/background cutnotseq_memechip_out/cut-not-seq.fa cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.246113
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 cutnotseq_memechip_out/combined.meme cutnotseq_memechip_out/combined.meme 1> cutnotseq_memechip_out/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.2268
Invoking:
  spamo -verbosity 1 -oc cutnotseq_memechip_out/spamo_out_1 -bgfile cutnotseq_memechip_out/background -primary TCAGSACCATGGACAGCDCCM cutnotseq_memechip_out/cut-not-seq.fa cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 1.716967
Invoking:
  spamo -verbosity 1 -oc cutnotseq_memechip_out/spamo_out_2 -bgfile cutnotseq_memechip_out/background -primary WMATTWRCATA cutnotseq_memechip_out/cut-not-seq.fa cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.310332
Invoking:
  spamo -verbosity 1 -oc cutnotseq_memechip_out/spamo_out_3 -bgfile cutnotseq_memechip_out/background -primary GGGMGGGRSCNGSGSSVGVGGSGSVGGVG cutnotseq_memechip_out/cut-not-seq.fa cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.355152
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutnotseq_memechip_out/fimo_out_1 --bgfile cutnotseq_memechip_out/background --motif TCAGSACCATGGACAGCDCCM cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/cut-not-seq.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.412256
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutnotseq_memechip_out/fimo_out_2 --bgfile cutnotseq_memechip_out/background --motif WMATTWRCATA cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/cut-not-seq.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.340944
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutnotseq_memechip_out/fimo_out_3 --bgfile cutnotseq_memechip_out/background --motif GGGMGGGRSCNGSGSSVGVGGSGSVGGVG cutnotseq_memechip_out/meme_out/meme.xml cutnotseq_memechip_out/cut-not-seq.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.436245
Writing output
Invoking:
  meme-chip_html_to_tsv cutnotseq_memechip_out/meme-chip.html cutnotseq_memechip_out/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.191598
Done