Chris Norman
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Activity overview
Latest activity by Chris Norman-
Chris Norman commented,
This kind of error is definitely caused by using newer versions of Java (i.e., 17+). The newest version that GATK is tested with currently is Java 11. So Java 8 or Java 11 are required; newer versi...
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Chris Norman commented,
Robert Bremel The BuildBamIndex issue you mentioned sounds very much like a separate (known) issue that is specific to `BuildBamIndex` (see https://github.com/broadinstitute/picard/issues/1827).
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Chris Norman commented,
Hi Eva (Evander). I'm a GATK developer, and was just looking at this. I would expect those relative paths to work, and indeed I tried a test locally with relative paths and it seems to work. Withou...
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Chris Norman commented,
Ok, thanks. I think that illustrates the problem - you're running version 1.19.5 of numpy, which is newer than the version GATK requires (you can see in the gatkcondaenv.yml file, where 1.17.5 is s...
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Chris Norman commented,
Ok, that looks the wrong version of numpy is present, or maybe that some underlying dependency has changed out from under us. Can you try (from within python, within the GATK conda env): import nu...
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Chris Norman commented,
Sayal Guirales Sorry you're having these issues with the conda env. As mentioned above, the original error message you referenced at the start of this thread definitely indicates that the python co...
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Chris Norman commented,
Hi @SkyWarrior Thanks for the updates. Have you had any success running the CNN/CNV tools using numpy 1.17 ? IIRC, I tried this previously (on Ubuntu) and the CNN tools failed and will require some...
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Chris Norman commented,
Hi SkyWarrior thanks for the movie and posting the solution. I think the numpy issue has been addressed (in the next release) by pinning it to 1.13.3 in the gatk env (longer term we probably need t...