outputs of cellScan

[ariannadib]

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.