Taxonomy assignment

[SRC151]

Hello Dr. Callahan,
As per the instructions, I downloaded the SILVA database (training set) and placed them in the directory containing the fastq files. Ran the command line: taxa <- assignTaxonomy(seqtab.nochim, "~/tax/silva_nr_v132_train_set.fa.gz", multithread=TRUE). But it does not work. I also tried the same with SILVA version 138.1, Could you please help me out with this matter? Is there something wrong on my part?

[benjjneb]

The filepath "~/tax/silva_nr_v132_train_set.fa.gz" needs to be replaced with the file path to the location of the training fastq file on your computer.

Where is the downloaded silva training set file on your computer?

[SRC151]

Hello Dr. Callahan, I replaced the "~" with the file path. It still shows an input/output error like this- Error: Input/Output no input files found dirPath: C:/Users/rc_sa/Downloads/MiSeq_SOP/tax/silva_nr_v132_train_set.fa.gz pattern: character(0)

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________________________________ From: Benjamin Callahan ***@***.***> Sent: 29 April 2024 10:55 To: benjjneb/dada2 ***@***.***> Cc: Sayantan Roy Choudhury ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [benjjneb/dada2] Taxonomy assignment (Issue #1938) The filepath "~/tax/silva_nr_v132_train_set.fa.gz" needs to be replaced with the file path to the location of the training fastq file on your computer. Where is the downloaded silva training set file on your computer? — Reply to this email directly, view it on GitHub<#1938 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BICL32W6WUY6TW5UO6SIO43Y7ZNNNAVCNFSM6AAAAABG2A4W62VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBSHE3DEMJRGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[benjjneb]

What is the output of the following?

ref_file <- "C:/Users/rc_sa/Downloads/MiSeq_SOP/tax/silva_nr_v132_train_set.fa.gz"
file.exists(ref_file)

[SRC151]

Dr. Callahan, It was a minor error I fixed it. I also ran the commands sent by you. The output is 'True'. Everything works fine. Thank you very much. Regards, Sayantan.

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________________________________ From: Benjamin Callahan ***@***.***> Sent: 30 April 2024 15:57 To: benjjneb/dada2 ***@***.***> Cc: Sayantan Roy Choudhury ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [benjjneb/dada2] Taxonomy assignment (Issue #1938) What is the output of the following? ref_file <- "C:/Users/rc_sa/Downloads/MiSeq_SOP/tax/silva_nr_v132_train_set.fa.gz" file.exists(ref_file) — Reply to this email directly, view it on GitHub<#1938 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BICL32SPNDU7NT62TGUVLHLY77ZRVAVCNFSM6AAAAABG2A4W62VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBWHE3DCNBWGU>. You are receiving this because you authored the thread.Message ID: ***@***.***>