Invoking:
  getsize cutrun_memechip_out/smooth.500.overlap.optimal.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.208045
Invoking:
  fasta-most -min 50 < cutrun_memechip_out/smooth.500.overlap.optimal.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.239365
Invoking:
  fasta-center -dna -len 100 < cutrun_memechip_out/smooth.500.overlap.optimal.fa 1> cutrun_memechip_out/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.280265
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: 0.118247
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: 0.200571
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 cutrun_memechip_out/smooth.500.overlap.optimal.fa cutrun_memechip_out/background
Finished invoke:
  name: bg  status: 0  time: 0.075066
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: 884.251014
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: 406.178777
Invoking:
  centrimo -seqlen 500 -verbosity 1 -oc cutrun_memechip_out/centrimo_out -bfile cutrun_memechip_out/background cutrun_memechip_out/smooth.500.overlap.optimal.fa cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.33117
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: 0.355575
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_1 -bgfile cutrun_memechip_out/background -primary GSHGCTGTCCRTGGTGCTGAA cutrun_memechip_out/smooth.500.overlap.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: 1.685964
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_2 -bgfile cutrun_memechip_out/background -primary ATGYWAAT cutrun_memechip_out/smooth.500.overlap.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: spamo2  status: 0  time: 5.772359
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_3 -bgfile cutrun_memechip_out/background -primary CYCYCYCYCYCYCYCTCYBYC cutrun_memechip_out/smooth.500.overlap.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: 5.439101
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_4 -bgfile cutrun_memechip_out/background -primary TRCATAW cutrun_memechip_out/smooth.500.overlap.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: 4.521726
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_5 -bgfile cutrun_memechip_out/background -primary TTYCTB cutrun_memechip_out/smooth.500.overlap.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: 7.788623
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_6 -bgfile cutrun_memechip_out/background -primary GGGYGGGR cutrun_memechip_out/smooth.500.overlap.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: 2.330959
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_7 -bgfile cutrun_memechip_out/background -primary ACAAADG cutrun_memechip_out/smooth.500.overlap.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: spamo7  status: 0  time: 3.88271
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_8 -bgfile cutrun_memechip_out/background -primary BTACCTGG cutrun_memechip_out/smooth.500.overlap.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: spamo8  status: 0  time: 0.935041
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_9 -bgfile cutrun_memechip_out/background -primary AGGCDG cutrun_memechip_out/smooth.500.overlap.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: spamo9  status: 0  time: 5.76909
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_10 -bgfile cutrun_memechip_out/background -primary AMATTCC cutrun_memechip_out/smooth.500.overlap.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: spamo10  status: 0  time: 2.764476
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_11 -bgfile cutrun_memechip_out/background -primary CACACSTG cutrun_memechip_out/smooth.500.overlap.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: spamo11  status: 0  time: 0.846968
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_1 --bgfile cutrun_memechip_out/background --motif GSHGCTGTCCRTGGTGCTGAA cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo1  status: 0  time: 2.764387
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_2 --bgfile cutrun_memechip_out/background --motif ATGYWAAT cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo2  status: 0  time: 1.818425
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_3 --bgfile cutrun_memechip_out/background --motif CYCYCYCYCYCYCYCTCYBYC cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo3  status: 0  time: 2.460564
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_4 --bgfile cutrun_memechip_out/background --motif TRCATAW cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo4  status: 0  time: 1.706445
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_5 --bgfile cutrun_memechip_out/background --motif TTYCTB cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo5  status: 0  time: 1.735583
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_6 --bgfile cutrun_memechip_out/background --motif GGGYGGGR cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo6  status: 0  time: 1.595358
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_7 --bgfile cutrun_memechip_out/background --motif ACAAADG cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo7  status: 0  time: 1.810152
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_8 --bgfile cutrun_memechip_out/background --motif BTACCTGG cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo8  status: 0  time: 1.605208
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_9 --bgfile cutrun_memechip_out/background --motif AGGCDG cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo9  status: 0  time: 1.484455
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_10 --bgfile cutrun_memechip_out/background --motif AMATTCC cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo10  status: 0  time: 1.674371
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_11 --bgfile cutrun_memechip_out/background --motif CACACSTG cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.500.overlap.optimal.fa
Finished invoke:
  name: fimo11  status: 0  time: 1.682702
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: 0.148191
Done