Error from a call to a function from IlluminaBeadArrayFiles

[mirrorlake999]

Hi there,

We have written a GWAS QC pipeline starting with GTC files.

Recently when we try to run this pipeline with a new .bpm file (Illumina Omni5Exome-4 v1.3), we encountered some errors.

The error is caused by a call to a function from IlluminaBeadArrayFiles, the gtc parsing library that Illumina made. It’s this call that’s causing the error:
norm = gtc.get_normalized_intensities(manifest.normalization_lookups)

Below is how I run the related code:

**>>> from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest, code2genotype

manifest_file = 'InfiniumOmni5Exome-4v1-3_A1.bpm'
gtc_file = '203423200004_R01C01.gtc'
gtc = GenotypeCalls(gtc_file)
manifest = BeadPoolManifest(manifest_file)
norm = gtc.get_normalized_intensities(manifest.normalization_lookups)
Traceback (most recent call last):
File "", line 1, in
File "IlluminaBeadArrayFiles/GenotypeCalls.py", line 581, in get_normalized_intensities
return [normalization_transforms[lookup].normalize_intensities(x_raw, y_raw) for (x_raw, y_raw, lookup) in zip(self.get_raw_x_intensities(), self.get_raw_y_intensities(), normalization_lookups)]
IndexError: list index out of range**

Here is the .bpm file used:
https://support.illumina.com/array/array_kits/infinium_humanomni5exome_beadchip_kit/downloads.html
Infinium Omni5Exome-4 v1.3 Manifest File (BPM Format - GRCh37)
185 MB
Nov 20, 2016

Attached is the testing etc file in the above code. Please note that you need to change the file extension from ".gtc.txt" to ".gtc" for testing.

Would you please take a look at the issue and help me with this request?

Thanks.

Jia

[jjzieve]

@mirrorlake999 Hi, sorry for the late response on this. This should be fixed in develop. Can you confirm?

[1teaspoon]

@jjzieve Hi I am receiving the same error as in the original post. From your reply sounds like this issue has been fixed recently? Would you please point me to version I can try out? Thank you!

[jjzieve]

@1teaspoon The develop branch should have this fix. If you're seeing this issue still, it might be something else? Can you post more details?

[1teaspoon]

@jjzieve Let me pull the latest develop and try it out. The version I am using is pretty old. Thanks!

[rmoran7]

Did this solve your issue ? This happened for me on the latest release and it is still an issue. Using a customer GSAv3 chip.

[jjzieve]

@rmoran7 I'd be surprised that this same issue is impacting a GSAv3 chip. The original issue had to do with byte-wrapping from a normalization lookup iirc, and would only impact large chips (e.g. Omni5). Can you post your error? Maybe there's a mismatch between the manifest used to generate the GTCs and the one used when calling this lib?

[rmoran7]

Thanks for this, there was a slightly different manifest used. Solved by re-downloading the original manifest. Thanks.