Jean Monlong

How to run samtools on gs object directly, to get a BAM slice fast (for example)

I've learned today how to get a slice of a BAM on an instance, without having to download the whole BAM and index first. I imagine that's what the IGV app does, but I couldn't find any documentatio...

• Jean Monlong
• Edited June 09, 2023 10:06
• 2 followers
• 1 comment
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1. Community
2. Active Feature Requests
3. Make larger-memory nodes available

We would also like to use instances with more memory, closer to 1Tb. The maximum that I could request with the current available machines is 768Gb using AMD Rome. I think that supporting Intel Ice ...

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• April 06, 2023 20:47
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1. Terra on Google Cloud
2. ...
3. Workflows setup
4. Saving storage costs by deleting intermediate files

We've had to do some cleaning up of temporary files in our workspaces manually and the provided notebook didn't always find files to "mop". We also wanted a bit more control, for eg protecting from...

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• March 06, 2023 22:04
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1. Community
2. General Discussion
3. Issue when docker pulls an image: "no space left on device"

Hi Samantha, That's good news. I've resubmitted my workflow, and it looks like it's working now. Some of the problematic tasks have finished. The others are running. No sign of the issue anymore. B...

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• January 10, 2023 18:08
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1. Community
2. General Discussion
3. Issue when docker pulls an image: "no space left on device"

Thanks for the help! Here is the info: - workspace: https://app.terra.bio/#workspaces/firecloud-cgl/hprc-evaluation- submission ID: 63f1e57a-5e9f-4413-b2be-53822fc1b8e5- workflow ID: 46a167c5-d263-...

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• January 09, 2023 17:03
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Issue when docker pulls an image: "no space left on device"

Hi, I'm experiencing a new error on a task of one of our workflows. The error message says: Task GiraffeDeepVariantFromGAM.runDeepVariantCallVariants:23:6 failed. The job was stopped before the co...

• Jean Monlong
• January 09, 2023 16:48
• 2 followers
• 4 comments
• 0 votes

1. Community
2. General Discussion
3. "HTTP Status 400 – Bad Request" when clicking on workflows.

Thanks for looking into this. If there is any way, even a temporary hack, to get around this issue, I would be very interested because it's a real blocker in my work now to not be able to launch an...

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• December 26, 2022 17:15
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