Projects cannot been loaded in SQMtools

[Selucote82]

Dear SqueezeMeta developers, here I'm again!

It's been impossible to load a project in RStudio in MacOSX after loading SQMtools. I tried with sq2zip.py after ending the SM pipe, and also deleting the "tables" directory and launching sqm2tables.py.

Afterwards, I tried to load the .zip project in mi MacOS laptop using RStudio and was impossible to load:

• PN4=loadSQM("~/Desktop/Genomics/Nanopore_RawData/PN4/PN4.zip")
  R Session Aborted. R encountered a fatal error. The session was terminated.

-PN4=loadSQMlite("/Desktop/Genomics/Nanopore_RawData/PN4/PN4.zip")
Error in loadSQMlite("/Desktop/Genomics/Nanopore_RawData/PN4/PN4.zip") :
Directory "~/Desktop/Genomics/Nanopore_RawData/PN4/PN4.zip" does not seem to contain valid SqueezeMeta tables
In this one trying sqm2tables.py too.

• Unzipping the PN4.zip in PN4_project directory created PN4=loadSQM("~/Desktop/Genomics/Nanopore_RawData/PN4/PN4_project")
  An error occurred while running sqm2tables.py

Any clue with this?

Thank you!

[fpusan]

PN4=loadSQM("~/Desktop/Genomics/Nanopore_RawData/PN4/PN4.zip") should be the right way to do it, but we've been having issues with some zip files in particular. Those can be traced back to limitations/bugs on how R handles zip files, I've looked for alternatives but haven't come to a solution yet. The issue normally raises an error when loading the project, instead of killing the R session, but maybe it's different in Mac...

Does PN4.zip still contain the tables? (i.e. it is the original zip file produced by sqm2zip.py). If so, unzipping it should work. See detailed instructions in #755

[Selucote82]

OK, it works! Indeed I really did the same thing you described in #755, but I unzipped the project in a directory with different name and there was the error.

Thank you!

[fpusan]

Glad to hear, and sorry for the inconvenience!