no output

[lihm1]

Dear veseshan, When I use snp-pileup, my output is nothing, and there is no wrong when I run it. I check my output file , the file output is as follows:

(R) [lccc@HPC-login out]$ zcat 909-WCMC11.out.gz 
Chromosome,Position,Ref,Alt,File1R,File1A,File1E,File1D,File2R,File2A,File2E,File2D

I do not know why my otput is nothing. My code is ./snp-pileup -g -q15 -Q20 -P100 -r25,0 common_all_20180418.vcf.gz ${path1}/909-WCMC11.out.gz ${path2}/SRR3146752.sorted.marked.BQSR.bam ${path2}/SRR3146775.sorted.marked.BQSR.bam can you tell me how to correct it? Thanks!

[jsha129]

This happened to me after waiting for 15 min and no output. However, i kept the tool running and it eventually produced results.