Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.044346
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.061687
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.087676
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.027948
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.078978
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background
Finished invoke:
  name: bg  status: 0  time: 0.025837
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 992.193549
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 29.400421
Invoking:
  centrimo -seqlen 475 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.14648
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.372419
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background -primary RGRTCMBSGGTTCGATYCCSV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.466978
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background -primary SCCVRDKKGKTARVGCGYMDGACTNHWAAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.420804
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background -primary ASSKVMHRTKMTRRCCRTTAMACTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.308337
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background -primary AAAAARWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.539944
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background -primary AGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.359312
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background -primary SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.475281
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background --motif RGRTCMBSGGTTCGATYCCSV /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.416111
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background --motif SCCVRDKKGKTARVGCGYMDGACTNHWAAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.413774
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background --motif ASSKVMHRTKMTRRCCRTTAMACTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.395451
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background --motif AAAAARWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.311535
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background --motif AGTGGTW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.283906
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/background --motif SAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/AWRI1631--MSS11.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.279665
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MSS11/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.177
Done