You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I'm trying to import picrust2 output. I have a tab-delimited text metadata file with two columns: SampleID and SampleType. I have the KO prediction files (pred_metagenome_unstrat.tsv.gz and pred_metagenome_unstrat_descrip.tsv.gz). I have set the working directory in R to the directory where all of these files are located.
Error in open.connection(file, "rt") : cannot open the connection
In addition: Warning message:
In open.connection(file, "rt") :
cannot open compressed file '', probable reason 'Invalid argument'
I have tried:
Specifying the full filepath.
Using the gzipped and unzipped versions of the prediction files.
Using the versions with and without the added description column.
Because I had renamed the files to specify traits and experiment, I reverted to the original filenames.
Regardless, I keep getting the same error. I can't see what I'm doing wrong here. Please advise. I've attached my metadata file and one of the picrust2 output files.
Note: The picrust2 output file was in tsv/tsv.gz format for this, but I had to convert to tab delimited .txt in order to upload it to github. This wasn't the format used in R. annual_KO_pred_metagenome_unstrat.txt metadata.txt
The text was updated successfully, but these errors were encountered:
Further note: I am using R 4.2.2 in RStudio in Windows 10. I am running RStudio as administrator. (Since sometimes Windows can be weird about write perms.)
I'm trying to import picrust2 output. I have a tab-delimited text metadata file with two columns: SampleID and SampleType. I have the KO prediction files (pred_metagenome_unstrat.tsv.gz and pred_metagenome_unstrat_descrip.tsv.gz). I have set the working directory in R to the directory where all of these files are located.
I ran the following commands:
sam_tab <- system.file(
"extdata", "metadata.txt",
package = "microbiomeMarker")
annual_KO_tab <- system.file(
"extdata",
"annual_KO_pred_metagenome_unstrat.tsv.gz",
package = "microbiomeMarker"
)
annual.ko <-
import_picrust2(
annual_KO_tab,
sam_tab,
trait = "KO"
)
And got the following error:
Error in open.connection(file, "rt") : cannot open the connection
In addition: Warning message:
In open.connection(file, "rt") :
cannot open compressed file '', probable reason 'Invalid argument'
I have tried:
Regardless, I keep getting the same error. I can't see what I'm doing wrong here. Please advise. I've attached my metadata file and one of the picrust2 output files.
Note: The picrust2 output file was in tsv/tsv.gz format for this, but I had to convert to tab delimited .txt in order to upload it to github. This wasn't the format used in R.
annual_KO_pred_metagenome_unstrat.txt
metadata.txt
The text was updated successfully, but these errors were encountered: