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Why there is 0 possible amplicon number in the output? #16

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Abieskawa opened this issue Dec 23, 2024 · 0 comments
Open

Why there is 0 possible amplicon number in the output? #16

Abieskawa opened this issue Dec 23, 2024 · 0 comments

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@Abieskawa
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Abieskawa commented Dec 23, 2024

Hi,
Thanks for developing so wonderful program. I want to ask why there is 0 possible amplicon number in the output? But it can still stick to the target? Please see the primer 0.
Screenshot 2024-12-23 at 19 54 32
Screenshot 2024-12-23 at 19 58 56

Here is my code. I incorporate to my preprocessing code, so it is in python form.

def run_command(command, description):
    """Run a shell command and handle errors."""
    print(f"Running: {description}")
    try:
        result = subprocess.run(command, shell=True, check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        if result.stdout:
            print(result.stdout.decode())
        if result.stderr:
            print(result.stderr.decode())
    except subprocess.CalledProcessError as e:
        print(f"Error during: {description}")
        print(e.stderr.decode())
        sys.exit(1)

run_command(
            f"primertool full {consensus_candidate_noN} {consensus_noN_genome} "
            f"--type SEQUENCE_INCLUDED_REGION --primer-num-retain 30 --check-multiplex "
            f"--checking-size-max 800 -p 8 -t {primer_output} --amplicon-num-max 5",
            f"Designing primers for {cid}"
        )

Many thanks~

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