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KChen-lab / Monopogen

SNV calling from single cell sequencing
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Error in Germline SNV calling #54

Open Teerapon789 opened 2 months ago

Teerapon789 commented 2 months ago

Hi,

I have been running preprocess step and then germline snv calling on my Mac. However, all my outputs in .gl.vcf.gz have zero bytes. Are there any errors? Would the problem be the different version of some packages? I also attached you log files from preprocess and germline calling steps. Thank you so much

log_MonopogenPreProcess.txt log_MonopogenGermlineCalling.txt

ariannadib commented 2 months ago

Hello! @Teerapon789 I have a similar problem but with the somatic module can I ask you at what point in the process did you generate the filter.targeted.bam files? in the preprocess module? Thanks in advance

jinzhuangdou commented 2 months ago

Could you type /Users/teeraponsahwangarrom/Downloads/Monopogen/apps/bgzip to see what happens? It seems the bgzip is not used conducted correctly in your Mac system. If so, you can move in a compatible version in you app folder

The filter.targeted.bam.file was generated on the cellScan step not the preprocess module.

Teerapon789 commented 2 months ago

@jinzhuangdou I re-ran this germline step again and I got .gl.vcf.gz file (28 bytes). Is it normal? Thank you so much

log_MonopogenGermline3.txt

jinzhuangdou commented 2 months ago

How many samples you are running? I see there are multiple channels in the logfile.

jinzhuangdou commented 2 months ago

Please use the latest version with region.lst set as chr1,chr2...chr22. It seems you are running a segmentation-based version (It is not necessary for small sample size).