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varvamp_log.txt
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varvamp_log.txt
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VARVAMP log
MODE = tiled
WARNING: small overlaps might hinder downstream analyses. Consider increasing.
ARG SETTINGS
THRESHOLD = 0.99875
PRIMER_ALLOWED_N_AMB = 2
AMPLICON_OPT_LENGTH = 260
AMPLICON_MAX_LENGTH = 365
MIN_OVERLAP = 1
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: 23 gaps with 162 nucleotides
Job: Creating consensus sequences.
Result: length of the consensus is 29831 nt
Job: Finding primer regions.
Result: 99.2 % of the consensus sequence will be evaluated for primers
Job: Digesting into kmers.
Result: 198981 kmers
Job: Filtering for primers.
Result: 18569 fw and 18958 rw potential primers
Job: Considering low scoring primers.
Result: 1024 fw and 1034 rw primers
Job: Finding potential amplicons.
Result: 3799 potential amplicons
Job: Creating amplicon scheme.
Result: 99.72 % total coverage with 112 amplicons
Job: Finalizing output.
Result: all done
varVAMP 0.9.4 finished in 105.466297 sec!
2023-10-17 16:12:47.679997