Primer3 issue with the Sequence_ID
0
0
Entering edit mode
12 days ago
aka ▴ 10

Hi everyone,

I am trying to sign primers for my sequences but I have an error that I do not understand the problem.

I made my finputfile.txt and I made the command below:

aka@aka:~/Desk/Primer$ /home/aka/primer3/src/primer3_core < input.txt > result.txt

input.txt

PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=20
PRIMER_MIN_SIZE=18
PRIMER_MAX_SIZE=23
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=100-150
P3_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/coralie/primer3/src/primer3_config/
=
SEQUENCE_ID=Qrob_P0702440.2
SEQUENCE_TEMPLATE=ATGCCTCCATCCTTCATCCACCGCCTACTCATCTCT....AATTGAGGAAGAGGGATTGTTCAATGAGTGGGAAGATTGCAAGACTTTGTTGA
=

It comes out: a results.txt file below, I feel like it's working but I have an error that shows up.

result.txt

    PRIMER_TASK=generic
    PRIMER_PICK_LEFT_PRIMER=1
    PRIMER_PICK_INTERNAL_OLIGO=0
    PRIMER_PICK_RIGHT_PRIMER=1
    PRIMER_OPT_SIZE=20
    PRIMER_MIN_SIZE=18
    PRIMER_MAX_SIZE=23
    PRIMER_MAX_NS_ACCEPTED=1
    PRIMER_PRODUCT_SIZE_RANGE=100-150
    P3_FILE_FLAG=1
    PRIMER_EXPLAIN_FLAG=1
    PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/coralie/primer3/src/primer3_config/
    PRIMER_ERROR=Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0
    =

When I change the SEQUENCE_ID to PRIMER_SEQUENCE_ID it doesn't work at all and shows me this:

PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=20
PRIMER_MIN_SIZE=18
PRIMER_MAX_SIZE=23
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=100-150
P3_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/coralie/primer3/src/primer3_config/
PRIMER_ERROR=Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0
=
PRIMER_SEQUENCE_ID=Qrob_P0702440.2
SEQUENCE_TEMPLATE=ATGCCTCCATCCTTCATCCACCGCCTACTCATCTCT....AATTGAGGAAGAGGGATTGTTCAATGAGTGGGAAGATTGCAAGACTTTGTTGA
PRIMER_ERROR=Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0
=
PRIMER_SEQUENCE_ID=test2
SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
PRIMER_ERROR=Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0
=
PRIMER_SEQUENCE_ID=test3
SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
PRIMER_ERROR=Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0
=

Do you know where this error comes from? Are my primers good in the first case with the error?

Thank you in advance for your help

Have a nice day

Aka

primer3 • 50 views
ADD COMMENT

Login before adding your answer.

Traffic: 3051 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6