Error in file.exists(file) : object 'data2_table.qza' not found

[yezi0721]

setwd("~/squencing_analyze/R_microeco_package")
qiime2meco(ASV_data = data2_table.qza, sample_data = sample-metadata.tvs, taxonomy_data = taxonomy.qza, phylo_tree = tree.qza)
Error in file.exists(file) : object 'data2_table.qza' not found.

I feel confused about how to transfer my QIIME2 data to microtable? Under my working directory, it shows the error above.

[ChiLiubio]

Is your feature table file named "data2_table.qza" and in your working directory?

[yezi0721]

Yes. I find the way to solve this problem. I need to add the whole file path in front of my file. Thank you.

…

On Wed, Apr 6, 2022 at 10:07 Chi Liu ***@***.***> wrote: Is your feature table file named "data2_table.qza" and in your working directory? — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APVCTQ33IGUGSTQX7CQPJ63VDWLBXANCNFSM5STUTSDA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Geize]

Hi @ChiLiubio and yezi0721,

Here it does not work. I have the same problem. I also tried to put the whole path as well, but without successful.

[ChiLiubio]

Hi @Geize ,
Could you provide more details about the error or problem? I am not sure what is the key point to the problem.

[Geize]

Hi @ChiLiubio,

Please, take a look - for qiime2 - using your script...

setwd("~/Documents/APlot/")

abund_file_path <- system.file("extdata", "~/Documents/APlot/tableDada2.qza", package="file2meco")
sample_file_path <-.....

qiime2meco(ASV_data = abund_file_path)

Error in read_qza(ASV_data) :
Input artifact () not found. Please check path and/or use list.files() to see files in current working directory.

list.files()
[1] "sample-metadata.tsv" "tableDada2.qza" "Taxonomy.qza"

Apparently, it only partial works when I use the same names that you indicate in your tutorial.

All the files were renamed according to your examples. Then, it works.

Going ahead, I got other issues.

I understood that I have to use unroot tree. Am I right?

Also, how should it name the fasta file with representative sequences?

Take a look on this:
[1] "dada2_rep_set.qza" "dada2_table.qza" "dna-sequences.fasta" "sample-metadata.tsv"
"taxonomy.qza" "tree.qza"

test1 <- qiime2meco(ASV_data = abund_file_path, sample_data = sample_file_path, taxonomy_data = taxonomy_file_path, phylo_tree = tree_data, rep_fasta = rep_data, auto_tidy = TRUE)

Error in self$tidy_dataset() :
No same feature name found among otu_table, tax_table and phylo_tree! Please check feature names in those objects !

In your code you write

please download fasta from https://docs.qiime2.org/2022.2/data/tutorials/pd-mice/dada2_rep_set.qza

the file name is 'dada2_rep_set.qza'

rep_data <- "dada2_rep_set.qza"

Here, it is fasta file or qza. To honest, I tried with both and nothing works.

[ChiLiubio]

Hi,
Please try this:
qiime2meco(ASV_data = "~/Documents/APlot/tableDada2.qza")
The system.file function is used to find the example file inside the package, maybe not what you need.

[mvtejesvi]

Hi @ChiLiubio,

I am having a similar problem, I am not sure how to solve it. Could you please help? When I try to import, it says the path to the artifact is not found, even though it is in the same directory. I also tried with full path, with no success. What could be the problem?

library(microeco)
d1 <-qiime2meco("table.qza")
No sample_table provided, automatically use colnames in otu_table to create one ...
d1
microtable-class object:
sample_table have 85 rows and 2 columns
otu_table have 3069 rows and 85 columns
dataset <- qiime2meco(ASV_data = "table.qza", sample_data = "metadata.tsv", taxonomy_data = "taxonomy.qza")
Error in read_qza(feature_table) : Path to artifact (.qza) not provided.

[ChiLiubio]

Hi. Please see the help document with command ?qiime2meco to check the parameter. I guess you are using file2meco v0.5.0. If yes, please see the help document and the latest tutorial (https://chiliubio.github.io/microeco_tutorial/file2meco-package.html#qiime2) to adjust the input parameters.