changlab / atac_mito_sc Goto Github PK

Hi,@jinxu937
Sorry to trouble you. I am trying to run "ATAC_mito_sc",but I have a problem and hope to get your help. I wonder how you got the "ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.Indel.vcf". I've been looking for a long time and haven't found it,I only found the "ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf"
If this is something you created, can you tell me how to create it? Thank you very much!

Best wishes!

Hi，when I use 1_scATAC_mito.sh script, I have the following problems, can you help me with these problems?

Adapter trimming: in-house script (02-12 19:45:47) elapsed: 0.0 TIME

Found lock file: /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/lock.raw__13-TAAGGCGA-GCGATCTA_R1.trim.fastq
Overwriting target...
Target to produce: /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/raw/13-TAAGGCGA-GCGATCTA_R1.trim.fastq
/bin/sh: /home/jinxu/pipeline_pypiper/ATAC_mito_sc/src/adapterTrimming: No such file or directory

/home/jinxu/pipeline_pypiper/ATAC_mito_sc/src/adapterTrimming /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/raw/13-TAAGGCGA-GCGATCTA_R1.fastq.gz /share/home/linlab/yangsuqin/ATAC-mito/test/example/outputtest/sc_output/13-TAAGGCGA-GCGATCTA/raw/13-TAAGGCGA-GCGATCTA_R2.fastq.gz (246493)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 246493; Command: /home/jinxu/pipeline_pypiper/ATAC_mito_sc/src/adapterTrimming; Return code: 127; Memory used: 0.0GB

Pipeline failed at: (02-12 19:45:47) elapsed: 0.0 TIME

Total time: 0:00:04
Failure reason: Subprocess returned nonzero result. Check above output for details
Traceback (most recent call last):
File "/share/home/linlab/yangsuqin/ATAC-mito/ATAC_mito_sc/src/scATACseq_mtSMC_3.py", line 107, in
pm.run(cmd,trimmed_fastq)
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 785, in run
self.callprint(cmd, shell, lock_file, nofail, container) # Run command
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 1028, in callprint
self._triage_error(SubprocessError(msg), nofail)
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 2131, in _triage_error
self.fail_pipeline(e)
File "/share/home/linlab/yangsuqin/.local/lib/python3.9/site-packages/pypiper/manager.py", line 1660, in fail_pipeline
raise exc
pypiper.exceptions.SubprocessError: Subprocess returned nonzero result. Check above output for details

Hi, I'm using the test datasets to try to run this pipeline and have had to do some troubleshooting because of the hg19 vs b37 resources listed on the scATACseq_mtSMC_3.yaml. I first tried the 1_scATAC_mito.sh with all the same resources as on your yaml file (except the MTIndel file, because I couldn't seem to find the exact one online), and I ran into the trouble because hg19 and b37 have a difference in the chromosome naming convention (chr1 vs 1). I've tried multiple combinations of things, and now I'm down to the dbSNPs and ref_TSS file being hg19 and everything else being b37 and finally got the 1_scATAC_mito.sh to run all the way through but there are no reads for genomeQ30PE_reads or Total_TSS_reads or mtQ30PE_reads. Could you shed some light as to how you resolved the hg19 vs b37 mix of resources?

Thank you!