Error in curl

[saulobritto]

Hi,

I'm trying to use the function

search_primer_pair

and keeps returning the error:

...
Error in curl::handle_setform(handle, .list = req$fields) : 
  Unsupported value type for form field 'id'.
1000 sequences retrieved from NCBI in 1 seconds, product length min:1 mean:1 max:1
1000 sequences aligned in 1 seconds length:2
pairwise DNA distances calculated in 0 seconds
constructed neighbor joining tree in 0 seconds

Anyone has any idea about how do I solve this?

primerTree version: 1.0.6 (latest)

Thanks in advance!

[MVesuviusC]

What primer sequences are you using? I'm guessing something might be off with the primers since it looks to be returning a bunch of 1bp sequences.

[saulobritto]

I'm using this pair:

Fish-F2: 5′-CATCCTACCTGTGGCAATCAC-3′
Fish-R2: 5′-TGGGCTCAG ACAATAAATCCT-3′

I'm using the function like this:

search_primer_pair(name=primer_name, forward, reverse,
                                         .parallel=T,
                                         api_key=API_KEY,
                                         num_aligns=1000,
                                         total_primer_specificity_mismatch=1)

[MVesuviusC]

I gave it a go and they worked for me. Perhaps NCBI's servers had a glitch? Try it again and if it doesn't work save the R object and put it in here so I can take a look at what might have gone wrong. Here is my output:

SauloPrimers.zip

[saulobritto]

That's weird. My guess is that one package has the wrong version, or is incompatible with some other, but I couldn't check all of them.
primerTree_run.zip

[MVesuviusC]

So it looks like for some reason in your blast results dataframe the accession column data are factors instead of characters, which is why the sequence retrieval step is failing. I'll try to tweak the code to enforce this column being a character. In the mean time, can you try reinstalling along with the dependencies? install.packages("primerTree", dependencies = TRUE) and see if that helps?

[saulobritto]

Sorry the delay. I tried to reinstall along with the dependencies and the error persists.

Thanks anyway for the momentary help but i will have to wait for the solution in the package hehe

[saulobritto]

Sorry to bother @MVesuviusC , but just to pass it on to my teacher, would you have any predictions for solving this problem?

Thanks!

[MVesuviusC]

Hey Saulo, sorry for the delay in looking at this, I've been scrambling with some other things. I'll try to work on this in the next week or two.

[MVesuviusC]

Hey Saulo, I updated the code to try to fix this error. Try installing primerTree from the "bug_issue_55" branch with 'devtools::install_github("MVesuviusC/primerTree", ref = "bug_issue_55")` and see if that works for you.