Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.136522
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.067156
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.096809
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.032425
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.076198
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background
Finished invoke:
  name: bg  status: 0  time: 0.031602
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 1000.875028
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 74.88502
Invoking:
  centrimo -seqlen 1956 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.164546
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.680984
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary DMBSGGRDTCGAACCSVGGAYCYYHBGRT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.487886
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary AGYCTGACGCSHTAMCCAHTDSGCYAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.433761
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary ACCAVC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.689523
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary AGMAGMT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.654527
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary TCWTCAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.735033
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary CAAGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.735883
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary RCGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.510317
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_8 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary GTGATAGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo8  status: 0  time: 0.273942
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_9 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary RATGGCAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo9  status: 0  time: 0.353163
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_10 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary AMAAGTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo10  status: 0  time: 0.520975
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/spamo_out_11 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background -primary AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml
Finished invoke:
  name: spamo11  status: 0  time: 0.727513
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif DMBSGGRDTCGAACCSVGGAYCYYHBGRT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.667401
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif AGYCTGACGCSHTAMCCAHTDSGCYAWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.707463
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif ACCAVC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.503244
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif AGMAGMT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.508146
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif TCWTCAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.507301
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif CAAGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.512181
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif RCGCCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.519712
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif GTGATAGY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo8  status: 0  time: 0.53282
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif RATGGCAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo9  status: 0  time: 0.542743
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif AMAAGTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo10  status: 0  time: 0.489432
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/background --motif AAAAWAT /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/RM11-1A--THP2.fa
Finished invoke:
  name: fimo11  status: 0  time: 0.507159
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--THP2/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.240348
Done