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Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF
Apache License 2.0
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using conda, can't get it to work because of some python bug #13

Closed martiliasf closed 6 years ago

martiliasf commented 6 years ago

ImportError: /nas/longleaf/home/martyf/.local/lib/python2.7/site-packages/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS2_AsUTF8String

my googling indicates the errors goes back to this

https://bugs.python.org/issue4434

KelleyRyanM commented 6 years ago

If you try to run a python script that contains only the line "import numpy", do you get the same error?

martiliasf commented 6 years ago

Yes, I get the same error.

martiliasf commented 6 years ago

Somehow fixed the error by playing with my system environment.

Now I have a new fun error. First, I used the .bpm manifest that was provided. Then the convert said that it can't use that to process indels, so I switched to the .csv manifest .... then, it gives me this nice error

2018-04-25 13:55:55,122 - GTC converter - WARNING - Provided manifest name: /pine/scr/m/a/martyf/GSA-24v1-0_A6.csv and manifest file used to generate GTC file: GSA-24v1-0_A2.bpm do not match, skipping

So i try to recreate the gtc files using https://github.com/Illumina/BeadArrayFiles , which of course doesn't seem to like using csv as manifests.

( edited to re-insert my ghost edit - my apologies)

KelleyRyanM commented 6 years ago

It looks like the CSV manifest (version A6) is different than the manifest that was used to create the GTC files (version A2). The most straight-forward fix would be to use the A2 version of the CSV format manifest. This is available for download at ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/productfiles/global-screening-array/v1-0/infinium-global-screening-array-24-v1-0-a2-manifest-file-csv.zip

As an aside, if you would like to create new GTC files with a new manifest, you would need to use the AutoConvert utility. The referenced BeadArrayFiles library can be used to read GTC files, but not create them. There is some additional detail on this at https://github.com/Illumina/BeadArrayFiles/blob/develop/README.md#generating-gtc-files under the section "Generating GTC files"

martiliasf commented 6 years ago

Thank you for your help. Things are converting!!