Invoking:
  getsize cutrun_memechip_out/smooth.243.idr.optimal.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.034156
Invoking:
  fasta-most -min 50 < cutrun_memechip_out/smooth.243.idr.optimal.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.099068
Invoking:
  fasta-center -dna -len 100 < cutrun_memechip_out/smooth.243.idr.optimal.fa 1> cutrun_memechip_out/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.087537
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: 0.016158
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: 0.073712
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 cutrun_memechip_out/smooth.243.idr.optimal.fa cutrun_memechip_out/background
Finished invoke:
  name: bg  status: 0  time: 0.018369
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: 695.569531
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: 100.692344
Invoking:
  centrimo -seqlen 487 -verbosity 1 -oc cutrun_memechip_out/centrimo_out -bfile cutrun_memechip_out/background cutrun_memechip_out/smooth.243.idr.optimal.fa cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.266624
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: 0.525307
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_1 -bgfile cutrun_memechip_out/background -primary GSSBDKGSHGCTGTCCRKGGTSCTGA cutrun_memechip_out/smooth.243.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: 0.694515
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_2 -bgfile cutrun_memechip_out/background -primary TCYTTTRWTATGCAAATKW cutrun_memechip_out/smooth.243.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: 2.293711
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_3 -bgfile cutrun_memechip_out/background -primary TATGCAAATGGCAYACCTRGTCCDAMCAA cutrun_memechip_out/smooth.243.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: 0.492707
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_4 -bgfile cutrun_memechip_out/background -primary GAATTTYC cutrun_memechip_out/smooth.243.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: 0.524729
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_5 -bgfile cutrun_memechip_out/background -primary AGGWA cutrun_memechip_out/smooth.243.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: 1.343994
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_6 -bgfile cutrun_memechip_out/background -primary ACARAGA cutrun_memechip_out/smooth.243.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: 0.592058
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_7 -bgfile cutrun_memechip_out/background -primary CCCACCC cutrun_memechip_out/smooth.243.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: spamo7  status: 0  time: 0.406654
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_8 -bgfile cutrun_memechip_out/background -primary RAAGAAA cutrun_memechip_out/smooth.243.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: spamo8  status: 0  time: 0.803723
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_9 -bgfile cutrun_memechip_out/background -primary AYAAAAGA cutrun_memechip_out/smooth.243.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: spamo9  status: 0  time: 0.510169
Invoking:
  spamo -verbosity 1 -oc cutrun_memechip_out/spamo_out_10 -bgfile cutrun_memechip_out/background -primary GTGGRGA cutrun_memechip_out/smooth.243.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: spamo10  status: 0  time: 1.36325
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_1 --bgfile cutrun_memechip_out/background --motif GSSBDKGSHGCTGTCCRKGGTSCTGA cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.616063
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_2 --bgfile cutrun_memechip_out/background --motif TCYTTTRWTATGCAAATKW cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.709802
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_3 --bgfile cutrun_memechip_out/background --motif TATGCAAATGGCAYACCTRGTCCDAMCAA cutrun_memechip_out/meme_out/meme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.826238
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_4 --bgfile cutrun_memechip_out/background --motif GAATTTYC cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.611035
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_5 --bgfile cutrun_memechip_out/background --motif AGGWA cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.530947
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_6 --bgfile cutrun_memechip_out/background --motif ACARAGA cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.566608
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_7 --bgfile cutrun_memechip_out/background --motif CCCACCC cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.596097
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_8 --bgfile cutrun_memechip_out/background --motif RAAGAAA cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.565583
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_9 --bgfile cutrun_memechip_out/background --motif AYAAAAGA cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.797631
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc cutrun_memechip_out/fimo_out_10 --bgfile cutrun_memechip_out/background --motif GTGGRGA cutrun_memechip_out/dreme_out/dreme.xml cutrun_memechip_out/smooth.243.idr.optimal.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.618971
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: 0.407865
Done