wakepy import set_keepawake, unset_keepawake # Ugly....

[DogCatSpace]

Hi,

Excited to use WGSE but ran into a problem. I installed Dev(eloper) v4+)successfully on a W10 machine but cannot get it to run. The error message is below. What is happening? Error message is below:

Starting WGS Extract on cygwin64 ... Traceback (most recent call last): File "E:\WGSExtract-Dev45_30Mar2024_installer\WGSExtractv4\program\wgsextract.py", line 109, in from mainwindow import set_output_path, set_BAM_file File "E:\WGSExtract-Dev45_30Mar2024_installer\WGSExtractv4\program\mainwindow.py", line 57, in from commandprocessor import run_bash_script File "E:\WGSExtract-Dev45_30Mar2024_installer\WGSExtractv4\program\commandprocessor.py", line 28, in from wakepy import set_keepawake, unset_keepawake # Ugly, but cannot import on Ubuntu aparently ImportError: cannot import name 'set_keepawake' from 'wakepy' (E:\WGSExtract-Dev45_30Mar2024_installer\WGSExtractv4\python\lib\site-packages\wakepy__init__.py) Press any key to continue . . .

[RandyHarr]

Rerun the installer. We were able to finally push out a release update to fix this issue that cropped up on all platforms. There had been a fix on the main website page. But all the releases are now patched. This only affected new installations or installations that did an update via the installer.

[DogCatSpace]

That was quick! and thanks. It worked! One more question. With Nebula, should I use the "Default" Ref. Library or use the CRAI file from Nebula?

[RandyHarr]

Nebula crai is fine and saves 30-60 minutes of processing on your own machine.

Not sure what you mean default ref library for Nebula. The tool should determine the existing ref Genome. The only time a default is chosen is if you hit the Realign button. There is no way to override the choice in that case.

[DogCatSpace]

Bravo on WGSE. As a microbiologist whom did his thesis in DNA fingerprinting in 1992, I can say this is extraordinary (that it is free is another astonishingly positive). I am slogging through the 2022 Manual and will restrict my questions to just two.

1. I see CombinedKit "can only be used at at GEDMatch..." If this is still correct, and with a RAW from Nebula, what is appropriate (23&Me, etc.) for Promethease? Safe to assume it is 23&Me version what?

2. It seems VCF files are best for InDel; Which Nebula input should I start with to charge-forward on InDel within WGS E? The nebula VCF file is ~450 MB and seems incompatible with Promethease analysis.

[RandyHarr]

I believe promethease can take a CombinedKit file. If not, 23andMeAPI is the next best. The more markers you can present, the more likely you have values for all that it can read. Do realize they only look at a small subset of markers (thousands). 23andMe v4 has the most markers but v3 and v5 have the more medically relevant ones; it seems. You can merge microarray result files using tools like from DNA Genics or Borland Genetics.

Most VCF files will have simple InDels. It depends on the vendor and their tool flow. Dante provided SNPs and InDels in separate VCFs for many years. Tools like Promethease do look at some InDels. The WGSE Microarray files do not generate InDel results at this time. I do not recall if Promethease takes in VCF files are not. You have to check with each tool site.

[DogCatSpace]

Thanks, importantly the 2022 WGS Extract Manual (pg 25) states "CombinedKit can only be used at [GEDMatch] and [Geneanet]. Does this mean that CombinedKit is likely to be accurate wherever used, but may not be accepted on some platforms?

[RandyHarr]

I will have to read that section of the manual for context. It seems that statement on limitations only applies to genetic genealogy sites.

Many sites are only setup to read a normal, single microarray result file of around 600k entries. The CombinedKit is over 2 million entries. A chip microarray is usually limited to testing around 1 million sites.