Invoking:
  getsize memechip_example_output_files/Klf1.fna 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.047661
Invoking:
  fasta-most -min 50 < memechip_example_output_files/Klf1.fna 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.116543
Invoking:
  fasta-center -dna -len 100 < memechip_example_output_files/Klf1.fna 1> memechip_example_output_files/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.225464
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 2 memechip_example_output_files/Klf1.fna memechip_example_output_files/background
Finished invoke:
  name: bg  status: 0  time: 0.033143
Invoking:
  meme memechip_example_output_files/seqs-centered -oc memechip_example_output_files/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 15 -bfile memechip_example_output_files/background -dna -seed 0 -p 8 -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 636.88811
Invoking:
  streme --verbosity 1 --oc memechip_example_output_files/streme_out -dna --seed 0 --p memechip_example_output_files/seqs-centered --minw 6 --maxw 15 --order 2
Finished invoke:
  name: streme  status: 0  time: 32.607975
Invoking:
  centrimo -seqlen 500 -verbosity 1 -oc memechip_example_output_files/centrimo_out -bfile memechip_example_output_files/background memechip_example_output_files/Klf1.fna memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/streme_out/streme.xml JASPAR2018_CORE_non-redundant.meme
Finished invoke:
  name: centrimo  status: 0  time: 32.246771
Invoking:
  tomtom -verbosity 1 -oc memechip_example_output_files/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc memechip_example_output_files/meme_out/meme.xml JASPAR2018_CORE_non-redundant.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 6.630276
Invoking:
  tomtom -verbosity 1 -oc memechip_example_output_files/streme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc memechip_example_output_files/streme_out/streme.xml JASPAR2018_CORE_non-redundant.meme
Finished invoke:
  name: streme_tomtom  status: 0  time: 7.384046
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 memechip_example_output_files/combined.meme memechip_example_output_files/combined.meme 1> memechip_example_output_files/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 4.692773
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_1 -bgfile memechip_example_output_files/background -keepprimary -primary WGGGTGTGGYYS memechip_example_output_files/Klf1.fna memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/streme_out/streme.xml
Finished invoke:
  name: spamo1  status: 0  time: 1.041532
Invoking:
  spamo -verbosity 1 -oc memechip_example_output_files/spamo_out_2 -bgfile memechip_example_output_files/background -keepprimary -primary NWGATAAG memechip_example_output_files/Klf1.fna memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/streme_out/streme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.886898
Invoking:
  fimo --verbosity 1 --oc memechip_example_output_files/fimo_out_1 --bgfile memechip_example_output_files/background --motif WGGGTGTGGYYS memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/Klf1.fna
Finished invoke:
  name: fimo1  status: 0  time: 0.748359
Invoking:
  fimo --verbosity 1 --oc memechip_example_output_files/fimo_out_2 --bgfile memechip_example_output_files/background --motif NWGATAAG memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/Klf1.fna
Finished invoke:
  name: fimo2  status: 0  time: 0.802032
Writing output
Invoking:
  meme-chip_html_to_tsv memechip_example_output_files/meme-chip.html memechip_example_output_files/summary.tsv "meme-chip -meme-p 8 -oc memechip_example_output_files -db JASPAR2018_CORE_non-redundant.meme Klf1.fna" 5.5.6 "Wed Jun 19 13\:59\:04 2024 -0700"
Finished invoke:
  name: summary  status: 0  time: 0.241072
Done
