Parsing PCR primers
FatemehA-bio opened this issue · comments
Dear Nextclade developers,
I faced this error when uploading customized primer file. I want to align a list of primers.
Could you please help me?
Thank you.
Best
Fatemeh
Error message: Error: When initializing Nextclade runner: When parsing PCR primers: CSV deserialize error: record 1 (line: 1, byte: 69): missing field Country (Institute): missing field Country (Institute)
Nextclade version 2.14.1 (commit: 85e00e8, branch: release)
Memory available: 2089 MBytes
User agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/109.0.0.0 Safari/537.36
Browser details: {"browser":{"name":"Chrome","version":"109.0.0.0"},"os":{"name":"Windows","version":"NT 10.0","versionName":"10"},"platform":{"type":"desktop"},"engine":{"name":"Blink"}}
Call stack:
Error: When initializing Nextclade runner: When parsing PCR primers: CSV deserialize error: record 1 (line: 1, byte: 69): missing field Country (Institute): missing field Country (Institute)
at M (https://clades.nextstrain.org/_next/static/chunks/68.daad1778960b5734.js:1:15774)
at https://clades.nextstrain.org/_next/static/wasm/cf835b4f9fbcf56c.wasm:wasm-function[1547]:0x1e3d5c
at new a (https://clades.nextstrain.org/_next/static/chunks/68.daad1778960b5734.js:1:9424)
at https://clades.nextstrain.org/_next/static/chunks/68.daad1778960b5734.js:1:24056
at u (https://clades.nextstrain.org/_next/static/chunks/444.170c49d0571b2ba1.js:1:28086)
at Generator._invoke (https://clades.nextstrain.org/_next/static/chunks/444.170c49d0571b2ba1.js:1:29376)
at a. [as next] (https://clades.nextstrain.org/_next/static/chunks/444.170c49d0571b2ba1.js:1:28489)
at p (https://clades.nextstrain.org/_next/static/chunks/68.daad1778960b5734.js:1:21841)
at d (https://clades.nextstrain.org/_next/static/chunks/68.daad1778960b5734.js:1:22038)
at https://clades.nextstrain.org/_next/static/chunks/68.daad1778960b5734.js:1:22097
How does your file look like?
This is the format that's used in Nextclade v2
https://github.com/nextstrain/nextclade_data/blob/049af8721b1f9d58a1ef3690afef31bfcf001069/data/datasets/sars-cov-2/references/MN908947/versions/2023-10-26T12%3A00%3A00Z/files/primers.csv?plain=1
However, PCR primer functionality will be removed from Nextclade v3. One of the reasons was that noone could figure out the format and it was rarely used feature as far as we can tell.
By the phrase "I want to align a list of primers." it is not entirely clear to me you understand what PCR primer mutation detection does in Nextclade.
Can you tell us a little how you use it and whether it will still be required in Nextclade v3 for your work? How do you imagine it should work? What input file formats would you like it to accept? This will help us to plan the upcoming changes better.