varvamp_log.txt

VARVAMP log 

MODE = tiled


ARG SETTINGS

THRESHOLD = 0.86
PRIMER_ALLOWED_N_AMB = 4
AMPLICON_OPT_LENGTH = 1500
AMPLICON_MAX_LENGTH = 2000
MIN_OVERLAP = 100

CONFIG SETTINGS

PRIMER_TMP = (56, 63, 60)
PRIMER_GC_RANGE = (35, 65, 50)
PRIMER_SIZES = (18, 24, 21)
PRIMER_HAIRPIN = 47
PRIMER_MAX_POLYX = 3
PRIMER_MAX_DINUC_REPEATS = 3
PRIMER_GC_END = (1, 3)
PRIMER_MAX_DIMER_TMP = 47
PRIMER_MIN_3_WITHOUT_AMB = 3
PCR_MV_CONC = 100
PCR_DV_CONC = 2
PCR_DNTP_CONC = 0.8
PCR_DNA_CONC = 15
PRIMER_TM_PENALTY = 2
PRIMER_GC_PENALTY = 0.2
PRIMER_SIZE_PENALTY = 0.5
PRIMER_MAX_BASE_PENALTY = 10
PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
PRIMER_PERMUTATION_PENALTY = 0.1

PROGRESS

Job:	 Checking config. 
Result:	 config file passed

Job:	 Preprocessing alignment and cleaning gaps. 
Result:	 21 gaps with 374 nucleotides

Job:	 Creating consensus sequences. 
Result:	 length of the consensus is 7446 nt

Job:	 Finding primer regions. 
Result:	 80.0 % of the consensus sequence will be evaluated for primers

Job:	 Digesting into kmers. 
Result:	 33640 kmers

Job:	 Filtering for primers. 
Result:	 4881 fw and 5394 rw potential primers

Job:	 Considering low scoring primers. 
Result:	 285 fw and 290 rw primers

Job:	 Finding potential amplicons. 
Result:	 5191 potential amplicons

Job:	 Creating amplicon scheme. 
Result:	 99.01 % total coverage with 5 amplicons

Job:	 Finalizing output. 
Result:	 all done 


varVAMP 0.9.4 finished in 103.540705 sec!
2023-10-19 16:31:10.756065