03g issue with cg07959070

[SiyiSEA]

This pull request addresses issue #13.

The script now checks if the chromosome (chr) column contains X, Y, MT, or PAR values and converts them as follows:

X is converted to 23 Y is converted to 24 MT is converted to 25 PAR are removed.

Additionally, to generate the Manhattan plot, the script ensures that the chromosome, p-value, and position columns are numeric, while the SNP column remains as a character type.

Please test the script before approving. Thanks! 😉

[drsora]

Ran it but I'm getting this error, not sure if it's related to the new code.

`Reading in /data/sonja/godmc/results/03/positive_control_untransformed_cg07959070.PHENO1.glm.linear.gz GWAS results [2024-10-17 15:19:51.870508] Exception: No write permission for directory: /tmp/RtmpGS8UZL

at #09. getWritablePathname.Arguments(static, ...)

• getWritablePathname.Arguments() is in environment 'R.utils'

  at #08. getWritablePathname(static, ...)

• getWritablePathname() is in environment 'R.utils'

  at #07. Arguments$getWritablePathname(pathname, mustNotExist = TRUE)

• Arguments$getWritablePathname() is local of the calling function

  at #06. popTemporaryFile.default(destnameT)

• popTemporaryFile.default() is in environment 'R.utils'

  at #05. popTemporaryFile(destnameT)

• popTemporaryFile() is in environment 'R.utils'

  at #04. decompressFile.default(file, decompFile <- tempfile(tmpdir = tmpdir), ext = NULL, FUN = FUN, remove = FALSE)

• decompressFile.default() is in environment 'R.utils'

  at #03. R.utils::decompressFile(file, decompFile <- tempfile(tmpdir = tmpdir), ext = NULL, FUN = FUN, remove = FALSE)

• R.utils::decompressFile() is in environment 'R.utils'

  at #02. fread(filename, header = T, data.table = F)

• fread() is in environment 'data.table'

  at #01. main()

• main() is in environment 'R_GlobalEnv'

Error: No write permission for directory: /tmp/RtmpGS8UZL`

[SiyiSEA]

/tmp/RtmpGS8UZL

Have you recognise this folder /tmp/RtmpGS8UZL?

It looks like this issue related with permission on your R/Linux environment.

[drsora]

/tmp/RtmpGS8UZL

Have you recognise this folder /tmp/RtmpGS8UZL?

It looks like this issue related with permission on your R/Linux environment.

That's odd, I've never had this kind of an issue and I also can't find the folder. I checked /tmp in general and it seems that I should have write permissions for it. I wonder why it even needs to write anything there though.

[SiyiSEA]

That's odd, I've never had this kind of an issue and I also can't find the folder. I checked /tmp in general and it seems that I should have write permissions for it. I wonder why it even needs to write anything there though.

Same odd to me😂. I ran the script well in the pipeline.

Have you ever try to run other R scripts under the same environment? Are they working?

[drsora]

Have you ever try to run other R scripts under the same environment? Are they working?

Weirdly enough, I ran 03f and it ran just fine 😅 I have no idea what's going on here. I'll try the mysterious, ancient trick of rebooting everything. I'll let you know if it's magically fixed.

Update, it did not fix it

[drsora]

apparently the issue is the fread function, it creates a temporary folder and my server seems to have an issue with that. I'm not the admin though so I have to see what I can do about it. I can try to read the data with a different function meanwhile, perhaps

I changed the function from read to read.csv and the whole thing ran fine. I think I have to see with our server admit if this tmp access issue can be fixed somehow.

[ejh243]

@drsora before we merge this change can you pull this branch and test Siyi's fix for 03g? Thanks

[ejh243]

@drsora it would also be helpful if you could rerun 02a and 02b to check that our fixes further up the pipeline do what they need to do.

[drsora]

@drsora before we merge this change can you pull this branch and test Siyi's fix for 03g? Thanks

I tested it and fixed the issues with my server, works perfectly now!