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10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
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Error starting VarTrix #45

Closed michelgw closed 4 years ago

michelgw commented 4 years ago

I am receiving a "Killed" error right after the loading cell barcodes step but not sure how to fix. My input is a 10x bam, barcodes file, dbSNP vcf, and reference fasta with log-level set to debug. Running VarTrix release v1.1.16 on an Ubuntu 16.04 server. Any suggestions on what might be going wrong? Thank you, Michelle

pmarks commented 4 years ago

Hi Michelle,

Can you send me the full screenshot of the command you invoked and the full result you got? Thanks!

Pat

On Fri, Apr 24, 2020 at 12:04 PM Michelle Webb notifications@github.com wrote:

I am receiving a "Killed" error right after the loading cell barcodes step but not sure how to fix. My input is a 10x bam, barcodes file, dbSNP vcf, and reference fasta with log-level set to debug. Running VarTrix release v1.1.16 on an Ubuntu 16.04 server. Any suggestions on what might be going wrong? Thank you, Michelle

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-- Patrick Marks Senior Director, Computational Biology patrick@10xgenomics.com name@10xgenomics.com [image: 10x Genomics] http://www.10xgenomics.com/ Office 925 123 4567 | Mobile 408 123 4567 6230 Stoneridge Mall Road Pleasanton, CA 94588-3260 | 10xgenomics.com http://www.10xgenomics.com/

michelgw commented 4 years ago

Hello Pat, sure:

error
pmarks commented 4 years ago

Hi Michelle,

Hmm, so usually the "Killed" message means that some other process on your machine or the Linux kernel killed the process for some reason, rather than it dying itself. You can read about some possible reaons here: https://stackoverflow.com/questions/726690/what-killed-my-process-and-why. Do you have a reasonable amount of free memory on your machine?

If you're able to share the input files you're using I could try them on our machine and see what happens.

Cheers, Pat

On Sat, Apr 25, 2020 at 9:49 PM Michelle Webb notifications@github.com wrote:

Hello Pat, sure:

[image: error] https://user-images.githubusercontent.com/31837356/80298172-527f0680-873e-11ea-9750-f5b4dc3f968d.png

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-- Patrick Marks Senior Director, Computational Biology patrick@10xgenomics.com name@10xgenomics.com [image: 10x Genomics] http://www.10xgenomics.com/ Office 925 123 4567 | Mobile 408 123 4567 6230 Stoneridge Mall Road Pleasanton, CA 94588-3260 | 10xgenomics.com http://www.10xgenomics.com/

michelgw commented 4 years ago

Hi Pat,

Sorry for the late response and thank you for the link. I think so...the server has 128GB of free memory. I tried running with a few different files and received the same result so it could very well just be the machine. If you're still able to test, I can share a set of example files.

Thank you, Michelle

pmarks commented 4 years ago

Hi Michelle,

Thanks for checking. It would be good to get to the bottom of this, if you're able to share all the input files. You can use the instructions here to send me large files: https://support.10xgenomics.com/docs/transfers fairly easily.

Or if you can provide a download link of some kind, I can get them.

Cheers, Pat

On Wed, Jun 3, 2020 at 3:13 PM Michelle Webb notifications@github.com wrote:

Hi Pat,

Sorry for the late response and thank you for the link. I think so...the server has 128GB of free memory. I tried running with a few different files and received the same result so it could very well just be the machine. If you're still able to test, I can share a set of example files.

Thank you, Michelle

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-- Patrick Marks Senior Director, Computational Biology patrick@10xgenomics.com name@10xgenomics.com [image: 10x Genomics] http://www.10xgenomics.com/ Office 925 123 4567 | Mobile 408 123 4567 6230 Stoneridge Mall Road Pleasanton, CA 94588-3260 | 10xgenomics.com http://www.10xgenomics.com/

michelgw commented 4 years ago

Sounds good, I can transfer using the redstone tool today. What email should I use to send the files?

Thanks, Michelle

pmarks commented 4 years ago

You can send them to patrick@10xGenomics.com.

Thanks, Pat

On Thu, Jun 4, 2020 at 9:36 AM Michelle Webb notifications@github.com wrote:

Sounds good, I can transfer using the redstone tool today. What email should I use to send the files?

Thanks, Michelle

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-- Patrick Marks Senior Director, Computational Biology patrick@10xgenomics.com name@10xgenomics.com [image: 10x Genomics] http://www.10xgenomics.com/ Office 925 123 4567 | Mobile 408 123 4567 6230 Stoneridge Mall Road Pleasanton, CA 94588-3260 | 10xgenomics.com http://www.10xgenomics.com/

michelgw commented 4 years ago

Great, thank you! The upload just completed.

Best, Michelle

pmarks commented 4 years ago

Hi Michelle,

Sorry for the delay. The issue is that you're consuming all the memory on the system attempting to load the VCF file you are working with. I noticed that the VCF is very large (16 GB compressed), and looks like it's a union of many samples. You will need to find some way to consider a smaller set of variants with vartrix. You could try running a variant caller directly on the BAM for example. Another option would be to intersect the variants with places that you have a reasonable amount of coverage in the BAM file. The runtime of vartrix is proportional to the number of variants you give it, so even if you were able to load all these variants, vartrix would take a prohibitively long time to run. Hope that helps!

Pat

On Thu, Jun 4, 2020 at 11:12 AM Michelle Webb notifications@github.com wrote:

Great, thank you! The upload just completed.

Best, Michelle

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-- Patrick Marks Senior Director, Computational Biology patrick@10xgenomics.com name@10xgenomics.com [image: 10x Genomics] http://www.10xgenomics.com/ Office 925 123 4567 | Mobile 408 123 4567 6230 Stoneridge Mall Road Pleasanton, CA 94588-3260 | 10xgenomics.com http://www.10xgenomics.com/

michelgw commented 4 years ago

Hello Pat,

Thank you so much for looking into this. That makes a lot of sense, I will try a smaller set of variants.

Best, Michelle