Invoking:
  getsize /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/mm10_ret_noTSS_filtered_500bp_labeled.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.49235
Invoking:
  fasta-most -min 50 < /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/mm10_ret_noTSS_filtered_500bp_labeled.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.259394
Invoking:
  fasta-center -dna -len 100 < /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/mm10_ret_noTSS_filtered_500bp_labeled.fa 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.366159
Invoking:
  fasta-shuffle-letters /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-centered /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.212552
Invoking:
  fasta-subsample /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-centered 600 -rest /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-discarded -seed 1 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.292604
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/mm10_ret_noTSS_filtered_500bp_labeled.fa /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/background
Finished invoke:
  name: bg  status: 0  time: 0.124038
Invoking:
  meme /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-sampled -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 30 -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 3434.01306
Invoking:
  dreme -v 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/dreme_out -png -dna -p /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-centered -n /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 11693.108542
Invoking:
  centrimo -seqlen 500 -verbosity 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/centrimo_out -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/background /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/mm10_ret_noTSS_filtered_500bp_labeled.fa /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/meme_out/meme.xml /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/dreme_out/dreme.xml /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MotifData/motif_databases/CIS-BP_2.00/Mus_musculus.meme
Finished invoke:
  name: centrimo  status: 0  time: 462.594212
Invoking:
  tomtom -verbosity 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/background /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/meme_out/meme.xml /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MotifData/motif_databases/CIS-BP_2.00/Mus_musculus.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 48.949245
Invoking:
  tomtom -verbosity 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/background /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/dreme_out/dreme.xml /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MotifData/motif_databases/CIS-BP_2.00/Mus_musculus.meme
Finished invoke:
  name: dreme_tomtom  status: 0  time: 9.381298
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/combined.meme /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/combined.meme 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 214.129799
Writing output
Invoking:
  meme-chip_html_to_tsv /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/meme-chip.html /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/Retina/mm10_ret_noTSS_filtered_500bp_labeled.MemeChipResults/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 3.263504
Done