Open snashraf opened 1 year ago
Hi Najeeb,
"test -w" tests if the user has write permissions to the align directory. It looks like your directory is read only. The pipeline needs to generate .idxstats and .count files for each sample (.bam file). If giving directory write permission is not an option, you create a new dir and symlink the bam/bai files.
Hi Daniela , Thanks! I was able to fix the issue.
I think there is some issue with gridss command . Can you please check that. I have to run the pipeline on 6000 samples and we have LSF system as scheduler. whats best way to run this pararelly?
Regards, Najeeb
On Fri, 23 Sept 2022, 20:39 Daniela Puiu, @.***> wrote:
Hi Najeeb,
"test -w" tests if the user has write permissions to the align directory. It looks like your directory is read only. The pipeline needs to generate .idxstats and .count files for each sample (.bam file). If giving directory write permission is not an option, you create a new dir and symlink the bam/bai files.
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Najeeb,
Have you set export HP_V=gridss in init.sh?
If so, the problem might be related to the R dependency $ which Rscript /usr/bin/Rscript
I have to update scripts/install_sysprerequisites.sh and add apt-get install -y -q r-base
################################################################################### For the large job, I would suggest running a few samples first and check the completion status.
Hi Daniela,
I was able to run the pipeline completely. I want to know which file I can use to understand the CN ( Copy Number ) information.
Regards, Najeeb
Hi Najeeb,
Glad you hear you have managed to run the pipeline.
Regarding mtDNA-CN :
Final count File:
out/count.tab # total reads & mtDNA-CN counts
Columns:
Run # Sample name
all # number of reads in the sample reads
mapped # number of aligned reads in the sample
MT # number of reads aligned to chrM
M # mtDNA copy number !!!
########################################################################
For each sample: scripts/filter.sh ; line 48 ; run idxstats2count.pl
cat $I.idxstats | \ idxstats2count.pl -sample $S -chrM $HP_RMT > $I.count
############################################################################
At the end, run the scripts/getSummary.sh ; line 15 ; run getCN.pl
cut -f2 $HP_IN | \ perl -ane 'print "$1.count\n" if(/(.+)./);' | xargs cat | cut -f1,2,3,4 | uniq.pl | \ getCN.pl > $ODIR/count.tab
Daniela Puiu
Bioinformatics Engineer
Department of Biomedical Engineering
Johns Hopkins University
From: Najeeb Ashraf Syed @.> Sent: Wednesday, September 28, 2022 7:18 AM To: dpuiu/MitoHPC @.> Cc: Daniela Puiu @.>; Comment @.> Subject: Re: [dpuiu/MitoHPC] Error while running Run.sh (Issue #3)
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Hi Daniela,
I was able to run the pipeline completely. I want to know which file I can use to understand the CN ( Copy Number ) information.
Regards, Najeeb
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Thanks, Daniela,
I have run the analysis, and these are the files generated by the MitoHPC. I just want to understand what each file contains. Why some files named as ".mutect2.mutect2"?
SI000020000010_02000865410.mutect2.00.vcf SI000020000010_02000865410.mutect2.fix.vcf SI000020000010_02000865410.mutect2.max.vcf SI000020000010_02000865410.mutect2.mutect2.00.vcf SI000020000010_02000865410.mutect2.mutect2.fix.vcf SI000020000010_02000865410.mutect2.mutect2.orig.vcf SI000020000010_02000865410.mutect2.mutect2.vcf SI000020000010_02000865410.mutect2.orig.vcf SI000020000010_02000865410.mutect2.vcf
By default MitoHPC runs 2 iteration. The 1st iteration output files are called sample.mutect2. whjile the 2nd iteration output files are called sample.mutect2.mutect2. In the 1st iteration , the rCRS sequence (chrM) is used as reference for alignment/SNV calling. For each sample, a new consensus sequence is generated , which is then used as reference in the 2nd iteration. Using the sample consensus should be better for accurate heteroplasmy calling. The 2nd iteration detects only heteroplamic SNVs. However, as output, we readjust the coordinates relative to rCRS and merge them withe the homoplasmies detected in the 1st iteration.
So if I want to have a final file containing both heteroplasmi and homoplasmi than file I should use? And same question also for mutserve?
Both SI000020000010_02000865410.mutect2.00.vcf and SI000020000010_02000865410.mutect2.mutect2.00.vcf will contain both homoplasmies and heteroplamies . However SI000020000010_02000865410.mutect2.mutect2.00.vcf should be more accurate,
Regarding mutserve, unfortunately it does not allow for a custom consensus sequence. If HP_M="mutserve", you need to set "HP_I=1"
Hey !!
I was trying to run the command and getting the below error.
` $HP_SDIR/run.sh > run.all.sh
Regards, Najeeb