Invoking:
  getsize /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.359301
Invoking:
  fasta-most -min 50 < /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.228424
Invoking:
  fasta-center -dna -len 100 < /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.fa 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.454913
Invoking:
  fasta-shuffle-letters /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.179921
Invoking:
  fasta-subsample /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered 600 -rest /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-discarded -seed 1 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.445859
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.fa /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/background
Finished invoke:
  name: bg  status: 0  time: 0.152106
Invoking:
  getsize /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_ALLNeuron_reproduciblePeaks_enhancerShort.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 2.79165
Invoking:
  fasta-center -dna -len 100 < /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_ALLNeuron_reproduciblePeaks_enhancerShort.fa 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered
Finished invoke:
  name: center_control  status: 0  time: 3.495239
Invoking:
  psp-gen -pos /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-sampled -neg /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered -minw 6 -maxw 20 -dna -revcomp 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/psp
Finished invoke:
  name: psp  status: 0  time: 4844.879926
Invoking:
  meme /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-sampled -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 30 -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/background -dna -psp /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/psp -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 4421.910765
Invoking:
  dreme -v 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/dreme_out -png -dna -p /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/seqs-centered -n /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/control-centered
Finished invoke:
  name: dreme  status: 0  time: 15853.671669
Invoking:
  centrimo -seqlen 501 -verbosity 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/centrimo_out -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/background -neg /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_ALLNeuron_reproduciblePeaks_enhancerShort.fa /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.fa /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/meme_out/meme.xml /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.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: 1985.72356
Invoking:
  tomtom -verbosity 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/background /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.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: 44.409479
Invoking:
  tomtom -verbosity 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/background /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.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: 2.6373
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/combined.meme /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/combined.meme 1> /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 23.772073
Writing output
Invoking:
  meme-chip_html_to_tsv /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/meme-chip.html /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MouseDNase/M1ScAtacSeqNEMO/BICCN_mouse_NEMO_snATAC-Seq_NP_reproduciblePeaks_enhancerShort.MemeChipResults/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.449518
Done