Invoking:
  getsize cluster_7_coord_nodup.txt.fa 1> $metrics
Finished invoke:
  name: count_primary_seqs  status: 0  time: 0.005684
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 0 -pseudo 1 cluster_7_coord_nodup.txt.fa ./background
Finished invoke:
  name: bg  status: 0  time: 0.004713
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_7_coord_nodup.txt.fa
Finished invoke:
  name: streme  status: 0  time: 4.893476
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 7137 -searchsize 100000 cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: meme  status: 0  time: 98.454805
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_7_coord_nodup.txt.fa
Finished invoke:
  name: sea_disc  status: 0  time: 0.115897
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_7_coord_nodup.txt.fa
Finished invoke:
  name: sea  status: 0  time: 2.867078
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_7_coord_nodup.txt.fa --m ./combined.meme
Finished invoke:
  name: distr_sea  status: 0  time: 0.444185
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: 0.6915
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: 1.554171
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 ./combined.meme ./combined.meme 1> ./motif_alignment.txt
Finished invoke:
  name: align_tomtom  status: 0  time: 1.712311
Invoking:
  fimo --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif 1-CTGGCTG streme_out/streme.xml cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.038853
Invoking:
  fimo --verbosity 1 --oc fimo_out_2 --bgfile ./background --motif 2-ATTTCAG streme_out/streme.xml cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.038559
Invoking:
  fimo --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif 4-AGCAGTTT streme_out/streme.xml cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.038304
Invoking:
  fimo --verbosity 1 --oc fimo_out_4 --bgfile ./background --motif 3-CTCWGAG streme_out/streme.xml cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.037955
Invoking:
  fimo --verbosity 1 --oc fimo_out_5 --bgfile ./background --motif CCYGCCTCWSCCTCY meme_out/meme.xml cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.07747
Invoking:
  fimo --verbosity 1 --oc fimo_out_6 --bgfile ./background --motif RGYGCCMYCTRGTGG meme_out/meme.xml cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.077906
Invoking:
  fimo --verbosity 1 --oc fimo_out_7 --bgfile ./background --motif 5-ATTGCCA streme_out/streme.xml cluster_7_coord_nodup.txt.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.038412
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_7_coord_nodup.txt.fa" 5.5.5 "Thu Sep 14 08\:48\:04 2023 +1000"
Finished invoke:
  name: summary  status: 0  time: 0.129661
Done
