pseudogene/lava-dna

LAVA (LAMP Assay Versatile Analysis) is an extendable open-source Loop-mediated isothermal AMPlification (LAMP)

lava-dna's Issues

latest primer3 does not work

seems that the thermo params file has now been embedded.

Tutorial

Good software and may I ask where can I find a tutorial on how to use it?
Regards,
Shaokang

Cannot declare the primer_config path

When running lava, I get this message: Parameter PRIMER_THERMODYNAMIC_PARAMETERS_PATH is not a valid Primer3 parameter. I made sure to copy the primer3 files to the correct folders according to the README file. Should I still set the PATH in my environment?

Below is the full output, using my own sequence alignment:

 ./lava.pl --alignment_fasta alignement.fasta --output_file output.txt
Enumerating outer forward primers

--------------------- WARNING ---------------------
MSG: Parameter PRIMER_THERMODYNAMIC_PARAMETERS_PATH is not a valid Primer3 parameter
---------------------------------------------------
Primer3Conserved getOligos had 0 oligos
  Generated "0" outer forward primers
Building outer reverse primers from outer forward primers
Enumerating loop "back" primers

--------------------- WARNING ---------------------
MSG: Parameter PRIMER_THERMODYNAMIC_PARAMETERS_PATH is not a valid Primer3 parameter
---------------------------------------------------
Primer3Conserved getOligos had 0 oligos
  Generated "0" loop "back" primers
Building loop "forward" primers from loop "back" primers
Enumerating middle forward primers

--------------------- WARNING ---------------------
MSG: Parameter PRIMER_THERMODYNAMIC_PARAMETERS_PATH is not a valid Primer3 parameter
---------------------------------------------------
Primer3Conserved getOligos had 0 oligos
  Generated "0" middle primers
Building middle reverse primers from middle forward primers
Enumerating inner forward primers

--------------------- WARNING ---------------------
MSG: Parameter PRIMER_THERMODYNAMIC_PARAMETERS_PATH is not a valid Primer3 parameter
---------------------------------------------------
Primer3Conserved getOligos had 0 oligos
  Generated "0" inner primers
Building inner reverse primers from inner forward primers
Analyzing outer forward primers
Analyzing outer reverse primers
Analyzing loop "forward" primers
Analyzing loop "back" primers
Analyzing middle forward primers
Analyzing middle reverse primers
Analyzing inner forward primers
Analyzing inner reverse primers
Sorting primer sets
Enumerating signatures
Iterating with groups: InnerF1, InnerR1, LoopF1, LoopR1, MiddleF1, MiddleR1, OuterF1, OuterR1
Building InnerF1 (at 60,  0->0)
Building InnerR1 (at 60,  0->0)
Building LoopF1 (at 50 0->0)
Building LoopR1 (at 50 0->0)
Building MiddleF1 (at 40 0->0)
Building MiddleR1 (at 40 0->0)
Building OuterF1 (at 50 0->0)
Building OuterR1 (at 50 0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF2, InnerR2, LoopF1, LoopR1, MiddleF1, MiddleR1, OuterF1, OuterR1
Building InnerF2 (at 80,  0->0)
Building InnerR2 (at 80,  0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF2, InnerR2, LoopF2, LoopR2, MiddleF1, MiddleR1, OuterF1, OuterR1
Building LoopF2 (at 70 0->0)
Building LoopR2 (at 70 0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF1, InnerR1, LoopF1, LoopR1, MiddleF2, MiddleR2, OuterF1, OuterR1
Building MiddleF2 (at 60 0->0)
Building MiddleR2 (at 60 0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF2, InnerR2, LoopF1, LoopR1, MiddleF2, MiddleR2, OuterF1, OuterR1
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF2, InnerR2, LoopF2, LoopR2, MiddleF2, MiddleR2, OuterF1, OuterR1
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF3, InnerR3, LoopF2, LoopR2, MiddleF2, MiddleR2, OuterF2, OuterR2
Building InnerF3 (at 90,  0->0)
Building InnerR3 (at 90,  0->0)
Building OuterF2 (at 70 0->0)
Building OuterR2 (at 70 0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF3, InnerR3, LoopF3, LoopR3, MiddleF2, MiddleR2, OuterF2, OuterR2
Building LoopF3 (at 80 0->0)
Building LoopR3 (at 80 0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF4, InnerR4, LoopF3, LoopR3, MiddleF2, MiddleR2, OuterF2, OuterR2
Building InnerF4 (at 94,  0->0)
Building InnerR4 (at 94,  0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF3, InnerR3, LoopF3, LoopR3, MiddleF2, MiddleR2, OuterF3, OuterR3
Building OuterF3 (at 80 0->0)
Building OuterR3 (at 80 0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF3, InnerR3, LoopF3, LoopR3, MiddleF3, MiddleR3, OuterF3, OuterR3
Building MiddleF3 (at 75 0->0)
Building MiddleR3 (at 75 0->0)
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Iterating with groups: InnerF4, InnerR4, LoopF3, LoopR3, MiddleF3, MiddleR3, OuterF3, OuterR3
Primer counts used for this plan iteration:
  0 Inner Forward
  0 Inner Reverse
  0 Loop Forward
  0 Loop Reverse
  0 Middle Forward
  0 Middle Reverse
  0 Outer Forward
  0 Outer Reverse

Faled to identify signatures - exiting normally

I've tried exporting the variable to the environment, and copying the files to what lava says it looks by default, but it doesn't change the result.

Run_LAVA_PARAMETERS_ON_LINUX

Hi Dear Bekaert,
I hope this message may find you well.
I have installed all the packages required to run LAVA on LINUX.
Unfortunately, I could not succeed to design primers because you have provided the PrimerLAVA Walkthrough file for designing LAMP primers or I do not know how to perform that analysis.
I kindly request to you for assistance so that I can download my gene of interest on Linux and design LAMP primers.

I look forward to hearing from you.

Syntax error near unexpected token `newline'

Hello,

When I try to run lava even with one of the test sequences provided (issuing ./lava.pl --alignment_fasta <s_aureus_consensus_segment.fasta> --output_file <output.txt>) I just get this simple error line in bash:

bash: syntax error near unexpected token `newline'

Info on my system:
Operating System: Manjaro Linux
Kernel: Linux 5.0.9-2-MANJARO
Architecture: x86-64
Perl: 5.28.2
Bioperl (-live and -run): 1.007001
Primer3: 2.4.0