Invoking:
  getsize ./all.fixed.TSS-upstream200bp.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.024908
Invoking:
  fasta-most -min 50 < ./all.fixed.TSS-upstream200bp.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.060312
Invoking:
  fasta-center -dna -len 100 < ./all.fixed.TSS-upstream200bp.fa 1> ./seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.084197
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 2 ./all.fixed.TSS-upstream200bp.fa ./background
Finished invoke:
  name: bg  status: 0  time: 0.018317
Invoking:
  meme ./seqs-centered -oc meme_out -mod zoops -nmotifs 50 -minw 6 -maxw 15 -bfile ./background -dna -searchsize 100000 -time 2919 -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 2788.445143
Invoking:
  streme --verbosity 1 --oc streme_out -dna --p ./seqs-centered --minw 6 --maxw 15 --time 4988 --order 2 --thresh 0.05 --totallength 4000000
Finished invoke:
  name: streme  status: 0  time: 77.805791
Invoking:
  centrimo -seqlen 500 -verbosity 1 -oc centrimo_out -bfile ./background -score 5.0 -ethresh 10.0 ./all.fixed.TSS-upstream200bp.fa meme_out/meme.xml streme_out/streme.xml db/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme db/MOUSE/uniprobe_mouse.meme db/EUKARYOTE/jolma2013.meme
Finished invoke:
  name: centrimo  status: 0  time: 87.875084
Invoking:
  tomtom -verbosity 1 -oc meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc meme_out/meme.xml db/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme db/MOUSE/uniprobe_mouse.meme db/EUKARYOTE/jolma2013.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 9.726828
Invoking:
  tomtom -verbosity 1 -oc streme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc streme_out/streme.xml db/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme db/MOUSE/uniprobe_mouse.meme db/EUKARYOTE/jolma2013.meme
Finished invoke:
  name: streme_tomtom  status: 0  time: 14.382559
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 ./combined.meme ./combined.meme 1> ./motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.096429
Invoking:
  spamo -verbosity 1 -oc spamo_out_1 -bgfile ./background -keepprimary -primary CGHCGVCGASG ./all.fixed.TSS-upstream200bp.fa meme_out/meme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo1  status: 0  time: 10.437062
Invoking:
  spamo -verbosity 1 -oc spamo_out_2 -bgfile ./background -keepprimary -primary GAGSAGTTCGW ./all.fixed.TSS-upstream200bp.fa meme_out/meme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo2  status: 0  time: 1.421815
Invoking:
  spamo -verbosity 1 -oc spamo_out_3 -bgfile ./background -keepprimary -primary 3-CGGTGATGHCGR ./all.fixed.TSS-upstream200bp.fa streme_out/streme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo3  status: 0  time: 9.033719
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif CGHCGVCGASG meme_out/meme.xml ./all.fixed.TSS-upstream200bp.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.627026
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_2 --bgfile ./background --motif GAGSAGTTCGW meme_out/meme.xml ./all.fixed.TSS-upstream200bp.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.580977
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif 3-CGGTGATGHCGR streme_out/streme.xml ./all.fixed.TSS-upstream200bp.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.578762
Writing output
Invoking:
  meme-chip_html_to_tsv ./meme-chip.html ./summary.tsv "meme-chip -oc . -time 240 -ccut 100 -fdesc description -dna -order 2 -minw 6 -maxw 15 -db db/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme -db db/MOUSE/uniprobe_mouse.meme -db db/EUKARYOTE/jolma2013.meme -meme-mod zoops -meme-nmotifs 50 -meme-searchsize 100000 -streme-pvt 0.05 -streme-totallength 4000000 -centrimo-score 5.0 -centrimo-ethresh 10.0 all.fixed.TSS-upstream200bp.fa" 5.4.1 "Sat Aug 21 19\:23\:23 2021 -0700"
Finished invoke:
  name: summary  status: 0  time: 0.104846
Done