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ppsp_output_screen [2017/05/04 10:35] (current)
hyjeong created
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 +====== PhyloPythiaS+ test running의 출력 화면 ======
 +결과물은 /​mnt/​apps/​pps/​tests/​test02/​에 위치한다.
 +
 +
 +  $ time ppsp -c /​apps/​pps/​tools/​config_ppsp_vm_refNCBI20140513_example.cfg -n -g -o s16 mg -t -p c -r -s
 +  Working contigs input fasta file created: /​apps/​pps/​tests/​test02/​working/​test_3strains.fna.ids
 +  Ids mapping for the working contigs fasta file created: /​apps/​pps/​tests/​test02/​working/​test_3strains.fna.cToIds
 +  Scaffolds -> contigs map ids file created: /​apps/​pps/​tests/​test02/​working/​test_3strains.fna.mapSCIds
 +  run Hidden Markov Model for (16S, 23S, 5S)
 +  run cmd: export PATH=/​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries:​$PATH;​ time /​mnt/​apps/​pps/​tools/​rna_hmm3/​rna_hmm3.py -i /​apps/​pps/​tests/​test02/​working/​test_3strains.fna.ids -o /​apps/​pps/​tests/​test02/​working/​test_3strains.fna.ids.gff
 +  28.62user 0.72system 0:​28.69elapsed 102%CPU (0avgtext+0avgdata 659792maxresident)k
 +  5792inputs+76208outputs (7major+145624minor)pagefaults 0swaps
 +  HMM return code: 0
 +  run (16S, 23S, 5S) classification
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​test_3strains.fna.ids.16S_rRNA.fna,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​silva115/​db/​ssu_115.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​silva115/​db/​ssu_115.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  107.81user 295.60system 14:​20.82elapsed 46%CPU (0avgtext+0avgdata 31695216maxresident)k
 +  30761616inputs+112outputs (499595major+6643608minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​test_3strains.fna.ids.23S_rRNA.fna,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​silva115/​db/​lsu_115.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​silva115/​db/​lsu_115.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  8.72user 9.29system 0:​19.63elapsed 91%CPU (0avgtext+0avgdata 3955792maxresident)k
 +  17392inputs+48outputs (94major+248212minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​test_3strains.fna.ids.5S_rRNA.fna,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​silva115/​db/​5S_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​silva115/​db/​5S_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.65user 3.41system 0:​05.53elapsed 91%CPU (0avgtext+0avgdata 1528272maxresident)k
 +  8inputs+48outputs (0major+96416minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run 31 marker gene analysis
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsE_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsE_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsE.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsE_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsE_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsE.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsE_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsE_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsE_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.38user 1.11system 0:​03.64elapsed 95%CPU (0avgtext+0avgdata 1449264maxresident)k
 +  0inputs+48outputs (0major+91506minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsC_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsC_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsC.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsC_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsC_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsC.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsC_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsC_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsC_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.26user 1.42system 0:​03.87elapsed 95%CPU (0avgtext+0avgdata 1428784maxresident)k
 +  0inputs+40outputs (0major+90377minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsB_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsB_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsB.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsB_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsB_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsB.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsB_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsB_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsB_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.52user 1.01system 0:​02.66elapsed 95%CPU (0avgtext+0avgdata 954976maxresident)k
 +  0inputs+48outputs (0major+60573minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsM_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsM_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsM.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsM_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsM_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsM.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsM_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsM_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsM_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.26user 0.99system 0:​03.37elapsed 96%CPU (0avgtext+0avgdata 1436944maxresident)k
 +  0inputs+40outputs (0major+90649minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsK_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsK_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsK.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsK_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsK_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsK.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsK_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsK_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsK_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.12user 0.56system 0:​01.77elapsed 95%CPU (0avgtext+0avgdata 679200maxresident)k
 +  0inputs+40outputs (0major+43412minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsJ_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsJ_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsJ.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsJ_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsJ_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsJ.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsJ_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsJ_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsJ_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.28user 0.93system 0:​03.31elapsed 97%CPU (0avgtext+0avgdata 1436976maxresident)k
 +  0inputs+48outputs (0major+90732minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsI_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsI_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsI.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsI_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsI_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsI.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsI_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsI_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsI_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.29user 0.97system 0:​03.38elapsed 96%CPU (0avgtext+0avgdata 1408256maxresident)k
 +  0inputs+40outputs (0major+88925minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplN_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplN_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplN.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplN_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplN_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplN.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplN_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplN_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplN_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.42user 0.84system 0:​03.38elapsed 96%CPU (0avgtext+0avgdata 1412352maxresident)k
 +  0inputs+40outputs (0major+89258minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​pyrG_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​pyrG_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​pyrG.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​pyrG_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​pyrG_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​pyrG.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​pyrG_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​pyrG_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​pyrG_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  3.24user 2.78system 0:​06.40elapsed 94%CPU (0avgtext+0avgdata 1540592maxresident)k
 +  0inputs+64outputs (0major+97930minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplL_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplL_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplL.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplL_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplL_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplL.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplL_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplL_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplL_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.54user 0.63system 0:​02.27elapsed 95%CPU (0avgtext+0avgdata 929344maxresident)k
 +  0inputs+40outputs (0major+59185minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplM_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplM_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplM.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplM_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplM_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplM.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplM_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplM_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplM_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.60user 0.72system 0:​02.43elapsed 96%CPU (0avgtext+0avgdata 983696maxresident)k
 +  0inputs+56outputs (0major+62384minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsS_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsS_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsS.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsS_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsS_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpsS.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpsS_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsS_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpsS_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.37user 0.84system 0:​03.30elapsed 97%CPU (0avgtext+0avgdata 1432864maxresident)k
 +  0inputs+40outputs (0major+90474minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplK_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplK_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplK.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplK_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplK_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplK.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplK_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplK_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplK_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.23user 1.11system 0:​03.46elapsed 96%CPU (0avgtext+0avgdata 1441072maxresident)k
 +  0inputs+40outputs (0major+91072minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplF_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplF_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplF.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplF_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplF_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplF.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplF_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplF_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplF_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.36user 1.18system 0:​03.67elapsed 96%CPU (0avgtext+0avgdata 1432880maxresident)k
 +  8inputs+48outputs (0major+90471minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplD_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplD_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplD.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplD_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplD_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplD.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplD_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplD_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplD_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.12user 1.49system 0:​03.76elapsed 96%CPU (0avgtext+0avgdata 1416448maxresident)k
 +  0inputs+40outputs (0major+89441minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplE_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplE_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplE.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplE_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplE_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplE.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplE_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplE_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplE_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.23user 1.26system 0:​03.61elapsed 96%CPU (0avgtext+0avgdata 1420544maxresident)k
 +  0inputs+40outputs (0major+89697minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplB_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplB_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplB.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplB_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplB_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplB.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplB_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplB_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplB_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.13user 1.74system 0:​04.05elapsed 95%CPU (0avgtext+0avgdata 1441056maxresident)k
 +  0inputs+56outputs (0major+90987minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplC_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplC_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplC.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplC_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplC_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplC.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplC_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplC_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplC_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.40user 1.28system 0:​03.82elapsed 96%CPU (0avgtext+0avgdata 1436976maxresident)k
 +  0inputs+48outputs (0major+90732minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplA_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplA_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplA.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplA_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplA_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplA.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplA_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplA_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplA_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.52user 0.96system 0:​02.59elapsed 95%CPU (0avgtext+0avgdata 950880maxresident)k
 +  0inputs+48outputs (0major+60319minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​tsf_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​tsf_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​tsf.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​tsf_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​tsf_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​tsf.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​tsf_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​tsf_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​tsf_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.15user 1.69system 0:​04.02elapsed 95%CPU (0avgtext+0avgdata 1441040maxresident)k
 +  0inputs+48outputs (0major+91144minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​frr_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​frr_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​frr.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​frr_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​frr_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​frr.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​frr_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​frr_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​frr_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.48user 0.82system 0:​02.40elapsed 95%CPU (0avgtext+0avgdata 921104maxresident)k
 +  0inputs+40outputs (0major+58502minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplT_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplT_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplT.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplT_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplT_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplT.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplT_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplT_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplT_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.62user 0.63system 0:​02.34elapsed 96%CPU (0avgtext+0avgdata 950880maxresident)k
 +  0inputs+48outputs (0major+60402minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​smpB_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​smpB_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​smpB.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​smpB_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​smpB_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​smpB.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​smpB_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​smpB_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​smpB_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.39user 1.04system 0:​03.58elapsed 95%CPU (0avgtext+0avgdata 1436960maxresident)k
 +  0inputs+40outputs (0major+90733minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​infC_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​infC_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​infC.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​infC_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​infC_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​infC.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​infC_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​infC_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​infC_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.26user 1.17system 0:​03.56elapsed 96%CPU (0avgtext+0avgdata 1404160maxresident)k
 +  0inputs+40outputs (0major+88668minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​pgk_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​pgk_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​pgk.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​pgk_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​pgk_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​pgk.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​pgk_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​pgk_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​pgk_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.25user 2.40system 0:​04.92elapsed 94%CPU (0avgtext+0avgdata 1552912maxresident)k
 +  0inputs+56outputs (0major+98045minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpoB_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpoB_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpoB.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpoB_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpoB_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpoB.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpoB_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpoB_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpoB_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  8.33user 4.33system 0:​13.28elapsed 95%CPU (0avgtext+0avgdata 1449312maxresident)k
 +  0inputs+64outputs (0major+91756minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplP_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplP_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplP.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplP_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplP_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplP.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplP_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplP_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplP_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  1.64user 0.73system 0:​02.46elapsed 96%CPU (0avgtext+0avgdata 996016maxresident)k
 +  0inputs+40outputs (0major+63246minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpmA_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpmA_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpmA.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpmA_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rpmA_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rpmA.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rpmA_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpmA_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rpmA_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.40user 0.78system 0:​03.27elapsed 97%CPU (0avgtext+0avgdata 1441072maxresident)k
 +  0inputs+48outputs (0major+90985minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplS_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplS_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplS.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplS_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​rplS_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​rplS.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​rplS_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplS_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​rplS_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.38user 0.93system 0:​03.42elapsed 96%CPU (0avgtext+0avgdata 1436960maxresident)k
 +  0inputs+40outputs (0major+90731minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​nusA_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​nusA_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​nusA.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​nusA_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​nusA_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​nusA.hmm ​ /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​nusA_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​nusA_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​nusA_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  2.53user 2.61system 0:​05.47elapsed 93%CPU (0avgtext+0avgdata 1598000maxresident)k
 +  0inputs+48outputs (0major+101271minor)pagefaults 0swaps
 +  mothur return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​dnaG_1.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​dnaG_1.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​dnaG.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: /​mnt/​apps/​pps/​tools/​hmmer-3.0/​binaries/​hmmsearch --domtblout /​apps/​pps/​tests/​test02/​working/​mgWorking/​dnaG_2.dom -E 0.01 -o /​apps/​pps/​tests/​test02/​working/​mgWorking/​dnaG_2.out /​mnt/​host_shared/​reference_NCBI20140513/​mg4/​hmmAmphora/​dnaG.hmm /​apps/​pps/​tests/​test02/​working/​mgWorking/​test_3strains.fna.ids.PROT
 +  HMM  return code: 0
 +  run cmd: time /​mnt/​apps/​pps/​tools/​mothur/​mothur1333/​mothur "#​classify.seqs(fasta=/​apps/​pps/​tests/​test02/​working/​mgWorking/​dnaG_dna.gff,​ template=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​dnaG_bact+arch_dna.fna,​ taxonomy=/​mnt/​host_shared/​reference_NCBI20140513/​mg4/​db/​dnaG_bact+arch_dna.tax,​ method=bayesian,​ cutoff=80, iters=300)"​
 +  4.06user 4.41system 0:​09.18elapsed 92%CPU (0avgtext+0avgdata 1465760maxresident)k
 +  0inputs+56outputs (0major+93112minor)pagefaults 0swaps
 +  mothur return code: 0
 +  Working contigs input fasta file without non-DNA chars created: /​apps/​pps/​tests/​test02/​working/​test_3strains.fna.ids
 +  Candidate placement of sequences by the
 +  16S:5
 +  23S:5
 +  5S:3
 +  all 16S, 23S, and 5S:10
 +  Candidate placement of sequences by the marker gene analysis (31): 67
 +  Sequences placed based on candidate placements, placed: 77
 +  Not assigned contigs of one scaffold are placed to the lowest common ancestor of assigned contigs, placed: 77
 +  Nodes--------------------------------------------
 +  65
 +  818
 +  265606
 +  817
 +  Sample specific data------------------------------------
 +  Summary-------------------------------------------------
 +  [243908, 22, '​Bacteria (2)', '​Bacteroidetes (976)',​ '​Bacteroidia (200643)',​ '​Bacteroidales (171549)',​ '​Bacteroidaceae (815)',​ '​Bacteroides (816)',​ '​Bacteroides thetaiotaomicron (818)'​]
 +  [181499, 20, '​Bacteria (2)', '​Chloroflexi (200795)',​ '​Chloroflexi (32061)',​ '​Herpetosiphonales (189772)',​ '​Herpetosiphonaceae (189773)',​ '​Herpetosiphon (64)', '​Herpetosiphon aurantiacus (65)']
 +  [122927, 21, '​Bacteria (2)', '​Planctomycetes (203682)',​ '​Planctomycetia (203683)',​ '​Planctomycetales (112)',​ '​Planctomycetaceae (126)',​ '​Rhodopirellula (265488)',​ '​Rhodopirellula baltica (265606)'​]
 +  [1172, 1, '​Bacteria (2)', '​Bacteroidetes (976)',​ '​Bacteroidia (200643)',​ '​Bacteroidales (171549)',​ '​Bacteroidaceae (815)',​ '​Bacteroides (816)',​ '​Bacteroides fragilis (817)'​]
 +  -------------------------------------------------
 +  PPS "​train"​ return code: 0
 +  PPS "​predict"​ contigs return code: 0
 +  Placed sequences after PPS predict: 2825
 +  ​
 +  real 143m33.053s
 +  user 73m22.907s
 +  sys 44m51.128s
 +  ​
  
ppsp_output_screen.txt · Last modified: 2017/05/04 10:35 by hyjeong