Invoking:
  getsize /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/Repeat.Alu.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.177806
Invoking:
  fasta-most -min 50 < /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/Repeat.Alu.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.37457
Invoking:
  fasta-center -dna -len 100 < /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/Repeat.Alu.fa 1> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.682279
Invoking:
  fasta-subsample /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/seqs-centered 600 -rest /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/seqs-discarded -seed 1 1> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 1.250221
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/Repeat.Alu.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/background
Finished invoke:
  name: bg  status: 0  time: 0.634192
Invoking:
  meme /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/seqs-sampled -oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/meme_out -mod anr -nmotifs 10 -minw 5 -maxw 50 -bfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 2043.873421
Invoking:
  centrimo -seqlen 50 -verbosity 1 -oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/centrimo_out -bfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/background /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/Repeat.Alu.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/meme_out/meme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MotifData/motif_databases/CIS-BP/Homo_sapiens.meme
Finished invoke:
  name: centrimo  status: 0  time: 4.010843
Invoking:
  tomtom -verbosity 1 -oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/background /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/meme_out/meme.xml /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MotifData/motif_databases/CIS-BP/Homo_sapiens.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 82.035097
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/combined.meme /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/combined.meme 1> /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 29.031532
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/meme-chip.html /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HumanGenome/Repeats/RepeatNames/Repeat.Alu.MemeChipResults/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.929362
Done