Error run mgatk

[tianchen2019]

i am sorry to bother you. My code is as follows

source ~/app/anaconda3/envs/mgatk/bin/activate
mgatk tenx -i /Sshare/tianchen/AML/3_sample_buce_merge/ZLH_10x_2/outs/possorted_bam.bam \
  -n ZLH -o ZLH_mgatk_50bp -c 8 \
  -bt CB -b /Sshare/tianchen/AML/3_sample_buce_merge/ZLH_10x_2/outs/filtered_peak_bc_matrix/barcodes.tsv

the error is as follows.

Fri Feb 11 16:21:19 CST 2022: mgatk v0.6.2
Fri Feb 11 16:21:20 CST 2022: Found bam file: /Sshare/tianchen/AML/3_sample_buce_merge/ZLH_10x_2/outs/possorted_bam.bam for genotyping.
Fri Feb 11 16:21:20 CST 2022: Found file of barcodes to be parsed: /Sshare/tianchen/AML/3_sample_buce_merge/ZLH_10x_2/outs/filtered_peak_bc_matrix/barcodes.tsv
Fri Feb 11 16:21:20 CST 2022: User specified mitochondrial genome matches .bam file
Fri Feb 11 19:25:14 CST 2022: Finished determining/splitting barcodes for genotyping.
Fri Feb 11 19:25:14 CST 2022: Genotyping samples with 8 threads
Error in checkGrep(grep(".A.txt", files)) :
  Improper folder specification; file missing / extra file present. See documentation
Calls: importMito -> checkGrep

the snakemake_tenx.log is as follows.

Building DAG of jobs...
Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:
/fshare2/tianchen/AML/mt_coverage/3_sample_mgatk
If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument.

[caleblareau]

Can you send an ls -lRth of the output folder?

[tianchen2019]

Can you send an ls -lRth of the output folder?

I have solved this problem. But a new phenomenon emerged. I have a sample that finds many G>C mutations using mgatk's method. However, other samples did not show this phenomenon.

[caleblareau]

Hm okay; I’ve never observed this before… what kind of libraries are your samples from?

On Feb 17, 2022, at 12:57 AM, tianchen2019 @.***> wrote:



Can you send an ls -lRth of the output folder?

I have solved this problem. But a new phenomenon emerged. I have a sample that finds many G>C mutations using mgatk's method. [image]https://user-images.githubusercontent.com/46451175/154438120-a36893fd-8930-4612-ac21-2753e783e97f.png However, other samples did not show this phenomenon. [image]https://user-images.githubusercontent.com/46451175/154440570-87975747-5b9f-465b-80ef-ab61319db3c5.png

— Reply to this email directly, view it on GitHubhttps://github.com/caleblareau/mgatk/issues/56#issuecomment-1042713842, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD32FYLRIJTPWZMHQSNWXA3U3SZ6ZANCNFSM5OEDOO5Q. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.Message ID: @.***>

[tianchen2019]

My sample is from the bone marrow of leukemia patients. And the sequencing method is mtscATAC-seq. The sequencing is PE50. mtscATAC-seq was performed according to the method of this article. https://www.nature.com/articles/s41587-020-0645-6 Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

[caleblareau]

Wild-- I've never seen anything like this. I'm not sure what even to suggest how to help-- this is very unusual.

[caleblareau]

I'm closing this issue now as I really don't have a comment but @tianchen2019 if you have anything else that you can uncover about this sample, do let me know