process mtDNA genotyping using scATAC-seq data from 10x multiome

[pxh251]

I am following the Wiki to run: (see the screenshot attached)

All my bam and tsv files are generated correctly but when I am trying run the .sh file attached, I encountered a .slurm file and it has been just stuck here forever.

Note: Since my scATAC-seq data is from the 10x multiome, is there a difference when processing scATAC from 10x multiome vs. only scATAC alone?

I really appreciate your help!

[caleblareau]

you want to specify the mitochondrial fasta is all. If you are using standard GRCh38, its actually built in (-g hg38). It's stalling out b/c you gave it the full genome as a reference instead of just mito

[pxh251]

Thank you very much for your response! I replace my fasta with -g hg38. However, it got stuck on the following step without any error reported:

May I ask about what's your thought on this? Thanks!

[pxh251]

Thank you very much for your response! I replace my fasta with -g hg38. However, it got stuck on the following step without any error reported: May I ask about what's your thought on this? Thanks!

Can I quickly follow up on this please? Thank you so much!

[caleblareau]

Hey sorry it’s not clear what you mean getting stuck here. It looks like it’s working as planned… is there output in the snakemake log?

On Mar 26, 2024, at 1:12 PM, pxh251 @.***> wrote:



Thank you very much for your response! I replace my fasta with -g hg38. However, it got stuck on the following step without any error reported: [Screenshot 2024-03-22 at 4 57 54 PM] https://private-user-images.githubusercontent.com/93609961/316166689-267e4300-2c62-4204-ad6a-b13b94aa594a.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.xySDpFZsp2i97-k70R_681U5ELVgqk_yucx2O6pyECU May I ask about what's your thought on this? Thanks!

Can I quickly follow up on this please? Thank you so much!

— Reply to this email directly, view it on GitHubhttps://github.com/caleblareau/mgatk/issues/91#issuecomment-2021017620, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD32FYKO737WDAPMJX3QVM3Y2GUBFAVCNFSM6AAAAABFDUOBYWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRRGAYTONRSGA. You are receiving this because you were assigned.Message ID: @.***>

[pxh251]

there's no output at all (no files generated, including any log files). The job just stopped by itself after 10min.

[caleblareau]

Probably rm -rf the .snakemake folder and retry then?

Caleb

On Mar 26, 2024, at 1:32 PM, pxh251 @.***> wrote:

there's no output at all (no files generated, including any log files). The job just stopped by itself after 10min.

— Reply to this email directly, view it on GitHubhttps://github.com/caleblareau/mgatk/issues/91#issuecomment-2021062590, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD32FYJG76O63EWK3IHPRRTY2GWKHAVCNFSM6AAAAABFDUOBYWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRRGA3DENJZGA. You are receiving this because you were assigned.Message ID: @.***>