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ppsp_output_screen

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