Invoking:
  getsize cutrun_memechip_out/smooth.500.idr.optimal.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.104862
Invoking:
  fasta-most -min 50 < cutrun_memechip_out/smooth.500.idr.optimal.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.102041
Invoking:
  fasta-center -dna -len 100 < cutrun_memechip_out/smooth.500.idr.optimal.fa 1> cutrun_memechip_out/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.136258
Invoking:
  fasta-shuffle-letters cutrun_memechip_out/seqs-centered cutrun_memechip_out/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.056129
Invoking:
  fasta-subsample cutrun_memechip_out/seqs-centered 600 -rest cutrun_memechip_out/seqs-discarded -seed 1 1> cutrun_memechip_out/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.114842
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/background
Finished invoke:
  name: bg  status: 0  time: 0.058126
Invoking:
  meme cutrun_memechip_out/seqs-sampled -oc cutrun_memechip_out/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile cutrun_memechip_out/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 831.582599
Invoking:
  dreme -v 1 -oc cutrun_memechip_out/dreme_out -png -dna -p cutrun_memechip_out/seqs-centered -n cutrun_memechip_out/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 88.751376
Invoking:
  centrimo -seqlen 861 -verbosity 1 -oc cutrun_memechip_out/centrimo_out -bfile cutrun_memechip_out/background cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.279085
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 cutrun_memechip_out/combined.meme cutrun_memechip_out/combined.meme 1> cutrun_memechip_out/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.341045
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_1 -bgfile cutrun_memechip_out/background -primary GGHGCTGTCCRTGGTGCTGAA cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.933067
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_2 -bgfile cutrun_memechip_out/background -primary WTTVWTATGCAAATK cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 1.475732
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_3 -bgfile cutrun_memechip_out/background -primary GGGSSSSGGGMBGNGSBVSGSDGBGGGVGV cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 1.066309
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_4 -bgfile cutrun_memechip_out/background -primary TACAHA cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 1.265031
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_5 -bgfile cutrun_memechip_out/background -primary AARGAAA cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 1.515476
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_6 -bgfile cutrun_memechip_out/background -primary GGTGGGR cutrun_memechip_out/smooth.500.idr.optimal.fa cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 1.63099
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_1 --bgfile cutrun_memechip_out/background --motif GGHGCTGTCCRTGGTGCTGAA cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.500.idr.optimal.fa
Finished invoke:
  name: fimo1  status: 0  time: 1.521166
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_2 --bgfile cutrun_memechip_out/background --motif WTTVWTATGCAAATK cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.500.idr.optimal.fa
Finished invoke:
  name: fimo2  status: 0  time: 1.271826
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_3 --bgfile cutrun_memechip_out/background --motif GGGSSSSGGGMBGNGSBVSGSDGBGGGVGV cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.500.idr.optimal.fa
Finished invoke:
  name: fimo3  status: 0  time: 1.519306
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_4 --bgfile cutrun_memechip_out/background --motif TACAHA cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.idr.optimal.fa
Finished invoke:
  name: fimo4  status: 0  time: 1.875751
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_5 --bgfile cutrun_memechip_out/background --motif AARGAAA cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.idr.optimal.fa
Finished invoke:
  name: fimo5  status: 0  time: 1.062393
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_6 --bgfile cutrun_memechip_out/background --motif GGTGGGR cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.idr.optimal.fa
Finished invoke:
  name: fimo6  status: 0  time: 1.015998
Writing output
Invoking:
  meme-chip_html_to_tsv cutrun_memechip_out/meme-chip.html cutrun_memechip_out/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.253211
Done