Pi-Chuan Chang

@gevro, you are setting max passes in your command. You can’t change this setting without using a model trained for a larger number of passes. Our current model only supports...

Hi @jkalleberg , Thank you for reaching out. The model ckpt you're using was older than v1.4. And you're right: in v1.4 we added an extra channel, and we haven't...

> @pichuan Thank you for the quick reply. That's a good tip to bypass the insert_size channel by default. Looking forward to your update, much appreciated. > > If I...

New model checkpoints associated with new releases will be under gs://deepvariant/models/DeepVariant as you noticed. I mentioned that starting from v1.4.0, you can see this file: ``` $ gsutil cat gs://deepvariant/models/DeepVariant/1.4.0/DeepVariant-inception_v3-1.4.0+data-wgs_standard/model.ckpt.example_info.json...

Hi @jkalleberg , please see See: https://gist.github.com/pichuan/7ad09bf1fa8f519facf6806eca835ea6 I'll close this issue for now. Feel free to open more issues if you have any questions or feedback for us.

Hi @yangyxt , can you try a command like: https://github.com/google/deepvariant/blob/r1.4/docs/deepvariant-quick-start.md#notes-on-singularity ?

If i recall correctly, there might be warnings but it didn't seem to affect the run. Can you confirm whether you're actually getting unexpected results or not? Thank you!

Thanks @yangyxt . Good to know that you're not seeing strange behaviors despite the warning messages. I'll close this issue now.

@yangyxt was this resolved? From the original error message, it seems to me that the input to call_variants was truncated. Which means that your make_examples run might have not been...

I'm not very familiar with SINGULARITY_CACHEDIR. But, in your command, if you're running it 3 times, you should use a different --intermediate_results_dir. Output of `make_examples` will be written to that...