Trouble with subsetTax function and error loading SQM

[kmarr037]

Hi! I hope you are doing well!

I have a project where I've been loading my SQM object as R data. So far I haven't had any issues but now when I try to subsetTax with this code I get the following error:

load("project_data.RDATA")>
actino <- subsetTax(project_data, "phylum", tax = "Actinomycetota", rescale_copy_number = FALSE) 
Error in if (SQM$misc$onlybins) { : argument is of length zero

I tried using <library(data.table)> and also got this error.

So then I tried to load in the actual file and not just the R data using the following code and got an error:

project_data <- loadSQM("./my_sqm_project") 

Loading total reads
Loading orfs
    table...
|--------------------------------------------------|
|==================================================|
    abundances...
    sequences...
|--------------------------------------------------|
|==================================================|
    taxonomy...
|--------------------------------------------------|
|==================================================|
Loading contigs
    table...
|--------------------------------------------------|
|==================================================|
    abundances...
    sequences...

Error in file.exists.zip(contigs_vecfile) : 
  argument "file_path" is missing, with no default

In addition: 
Warning message:
In loadSQM_(project_path, tax_mode, tax_source, trusted_functions_only,  :
  Your project was created with SqueezeMeta v1.6.5, while this is SQMtools v1.8.0. You can ignore this message if things are working fine for you, but if you experience any issue consider using the right version of SQMtools for this project> 

Is there a way I can fix either the R data or try to load in the file with loadSQM by going back to SqeezeMeta v1.6.5?

Thank you for your help in advance!!

[fpusan]

The second error during loadSQM seems like a duplicate of #1041 and should be fixed in our dev version
conda create -n SqueezeMeta-dev -c conda-forge -c bioconda -c fpusan squeezemeta-dev=1.8.1
Let me know if this fixes it for you

[kmarr037]

Thank you for your reply! This may be a dumb question, so I apologize, but running the dev version requires re-running the data through SqueezeMeta from the beginning, correct?

[fpusan]

Not necessarily. You can just create the environment with the dev version, activate it, open R and load SQMtools. Then try to load your existing project using loadSQM.

[fpusan]

Did it work?