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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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outputs of cellScan #53

Open ariannadib opened 2 months ago

ariannadib commented 2 months ago

Hello! I am writing to ask you if you could list me what the outputs of each of the three somatic modules should be. In fact, after the cellscan module I get the following warning: INFO Monopogen.py Get single cell level information from sequencing data... INFO:main:Get single cell level information from sequencing data... [main_samview] region "-o" specifies an unknown reference name. Continue anyway. [main_samview] region "/Users/Arianna/Monopogen/out_D545/Bam/chr1.filter.targeted.bam" specifies an unknown reference name. Continue anyway. after that in the out/bam folder I find a merged.bam and merged.bam.bai and a split_bam folder with .bam files related to each cell. In the out/somatic folder I find the following files: ch1.bed, ch1.gl.vcf.DP4, ch1.gl.vcf.filter.DP4, chr1.gl.vcf.filter.hc.bed, chr1.gl.vcf .filter.hc.pos. When I try to launch ldrefinement I get the following error: File 'out_D545/somatic/chr1.gl.filter.hc.cell.mat.gz' does not exist or is non-readable. getwd()=='/Users/Arianna/Monopogen' this file was in fact not produced in the previous module. I would like to ask if you have any ideas as to why the cellScan module may not have given the full output. Thank you and I apologize if in the previous issues I was not clear enough in describing the problem.

jinzhuangdou commented 2 months ago

Are you using the latest version? In the new version, bamsplit step is not necessary and the split_bam file will not be available. The old version has huge computational burden and the cellscan step is likely to fail. Could you try the updated version to see what happens? Thanks

ariannadib commented 2 months ago

Hi, thanks for the reply, I'm now using the new version but I still don't have targeted.filter.files as output, I don't know exactly at what point this file should be created but it still seems necessary for the cellScan module to create the .mat file . Can you tell me at what point this file should be generated? Could it be a problem of not enough space?

Thank you

ariannadib commented 2 months ago

It would be very useful to know what the outputs of each somatic module should be, both in the old and new versions. So as to be able to isolate the error, understanding which file is missing or incorrect and at what point it is generated

Thanks for your help