Invoking:
  getsize ./all.fixed.TSS-100bp.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.014275
Invoking:
  fasta-most -min 50 < ./all.fixed.TSS-100bp.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.045498
Invoking:
  fasta-center -dna -len 100 < ./all.fixed.TSS-100bp.fa 1> ./seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.062888
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 2 ./all.fixed.TSS-100bp.fa ./background
Finished invoke:
  name: bg  status: 0  time: 0.010442
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: 2801.718307
Invoking:
  streme --verbosity 1 --oc streme_out -dna --p ./seqs-centered --minw 6 --maxw 15 --time 4982 --order 2 --thresh 0.05 --totallength 4000000
Finished invoke:
  name: streme  status: 0  time: 71.61271
Invoking:
  centrimo -seqlen 200 -verbosity 1 -oc centrimo_out -bfile ./background -score 5.0 -ethresh 10.0 ./all.fixed.TSS-100bp.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: 36.765859
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: 20.775519
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: 13.807983
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 ./combined.meme ./combined.meme 1> ./motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 1035.971086
Invoking:
  spamo -verbosity 1 -oc spamo_out_1 -bgfile ./background -keepprimary -primary 2-BATGASCGACVMCGM ./all.fixed.TSS-100bp.fa streme_out/streme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.046425
Invoking:
  spamo -verbosity 1 -oc spamo_out_2 -bgfile ./background -keepprimary -primary 10-CGTCCATACGCG ./all.fixed.TSS-100bp.fa streme_out/streme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.046765
Invoking:
  spamo -verbosity 1 -oc spamo_out_3 -bgfile ./background -keepprimary -primary 4-AACRSTTWT ./all.fixed.TSS-100bp.fa streme_out/streme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.045669
Invoking:
  spamo -verbosity 1 -oc spamo_out_4 -bgfile ./background -keepprimary -primary TCARTACATMAMAAA ./all.fixed.TSS-100bp.fa meme_out/meme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.047075
Invoking:
  spamo -verbosity 1 -oc spamo_out_5 -bgfile ./background -keepprimary -primary 6-CACCTCC ./all.fixed.TSS-100bp.fa streme_out/streme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.044309
Invoking:
  spamo -verbosity 1 -oc spamo_out_6 -bgfile ./background -keepprimary -primary 1-CGASGMCGACGACGA ./all.fixed.TSS-100bp.fa streme_out/streme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.045846
Invoking:
  spamo -verbosity 1 -oc spamo_out_7 -bgfile ./background -keepprimary -primary GTCTGCTTGCTGAAG ./all.fixed.TSS-100bp.fa meme_out/meme.xml meme_out/meme.xml streme_out/streme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.048753
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif 2-BATGASCGACVMCGM streme_out/streme.xml ./all.fixed.TSS-100bp.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.219893
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_2 --bgfile ./background --motif 10-CGTCCATACGCG streme_out/streme.xml ./all.fixed.TSS-100bp.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.212675
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif 4-AACRSTTWT streme_out/streme.xml ./all.fixed.TSS-100bp.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.20963
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_4 --bgfile ./background --motif TCARTACATMAMAAA meme_out/meme.xml ./all.fixed.TSS-100bp.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.216149
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_5 --bgfile ./background --motif 6-CACCTCC streme_out/streme.xml ./all.fixed.TSS-100bp.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.189518
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_6 --bgfile ./background --motif 1-CGASGMCGACGACGA streme_out/streme.xml ./all.fixed.TSS-100bp.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.235733
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_7 --bgfile ./background --motif GTCTGCTTGCTGAAG meme_out/meme.xml ./all.fixed.TSS-100bp.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.222131
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-100bp.fa" 5.4.1 "Sat Aug 21 19\:23\:23 2021 -0700"
Finished invoke:
  name: summary  status: 0  time: 9.238727
Done