Invoking:
  getsize cluster_6_coord_nodup.txt.fa 1> $metrics
Finished invoke:
  name: count_primary_seqs  status: 0  time: 0.005692
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 0 -pseudo 1 cluster_6_coord_nodup.txt.fa ./background
Finished invoke:
  name: bg  status: 0  time: 0.004883
Invoking:
  streme --verbosity 1 --oc streme_out -dna --minw 6 --maxw 15 --order 0 --bfile ./background --seed 0 --align center --time 4740 --totallength 4000000 --evalue --thresh 0.05 --p cluster_6_coord_nodup.txt.fa
Finished invoke:
  name: streme  status: 0  time: 1.897691
Invoking:
  meme -oc meme_out -mod zoops -minw 6 -maxw 15 -bfile ./background -markov_order 0 -seed 0 -dna -revcomp -evt 0.05 -nostatus -time 7139 -searchsize 100000 cluster_6_coord_nodup.txt.fa
Finished invoke:
  name: meme  status: 0  time: 19.510675
Invoking:
  sea --verbosity 1 --oc sea_disc_out --qvalue --thresh 1 --order 0 --bfile ./background --seed 0 --align center --motif-pseudo 0.01 --noseqs --m meme_out/meme.xml --m streme_out/streme.xml --p cluster_6_coord_nodup.txt.fa
Finished invoke:
  name: sea_disc  status: 0  time: 0.050708
Invoking:
  sea --verbosity 1 --oc sea_out --thresh 0.05 --order 0 --bfile ./background --seed 0 --align center --motif-pseudo 0.01 --m meme_out/meme.xml --m streme_out/streme.xml --m db/motif_databases/HUMAN/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme --p cluster_6_coord_nodup.txt.fa
Finished invoke:
  name: sea  status: 0  time: 1.197748
Invoking:
  sea --verbosity 1 --oc distr_out --pvalue --thresh 1 --hofract 0 --order 0 --bfile ./background --seed 0 --motif-pseudo 0.01 --no-pgc --p cluster_6_coord_nodup.txt.fa --m ./combined.meme
Finished invoke:
  name: distr_sea  status: 0  time: 0.044355
Invoking:
  tomtom -verbosity 1 -oc streme_tomtom_out -min-overlap 5 -dist ed -evalue -thresh 1 -no-ssc streme_out/streme.xml db/motif_databases/HUMAN/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme
Finished invoke:
  name: streme_tomtom  status: 0  time: 0.475114
Invoking:
  tomtom -verbosity 1 -oc meme_tomtom_out -min-overlap 5 -dist ed -evalue -thresh 1 -no-ssc meme_out/meme.xml db/motif_databases/HUMAN/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme
Finished invoke:
  name: meme_tomtom  status: 0  time: 1.538438
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 ./combined.meme ./combined.meme 1> ./motif_alignment.txt
Finished invoke:
  name: align_tomtom  status: 0  time: 0.048637
Invoking:
  fimo --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif 1-NCCATCW streme_out/streme.xml cluster_6_coord_nodup.txt.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.027357
Invoking:
  fimo --verbosity 1 --oc fimo_out_2 --bgfile ./background --motif 2-ACARWGA streme_out/streme.xml cluster_6_coord_nodup.txt.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.027008
Invoking:
  fimo --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif AGRRAGGVAGAGADG meme_out/meme.xml cluster_6_coord_nodup.txt.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.044215
Writing output
Invoking:
  xstreme_html_to_tsv ./xstreme.html ./xstreme.tsv "xstreme --oc . --time 240 --streme-totallength 4000000 --meme-searchsize 100000 --dna --order 0 --evt 0.05 --minw 6 --maxw 15 --align center --meme-mod zoops --m db/motif_databases/HUMAN/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme --p cluster_6_coord_nodup.txt.fa" 5.5.5 "Thu Sep 14 08\:48\:04 2023 +1000"
Finished invoke:
  name: summary  status: 0  time: 0.090398
Done
