mgatk
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caleblareau
process mtDNA genotyping using scATAC-seq data from 10x multiome
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!
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
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!
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!
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: @.***>
there's no output at all (no files generated, including any log files). The job just stopped by itself after 10min.
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: @.***>