ASM step takes very long on a subsetted bam ~59 million reads #65
Description
I am running CGMAPTOOLS to get ASM calls from WGBS data on my sample. I ran the CGMAP step to convert to the ATCG format, performed SNV calling (bayes mode) and eventually submitted the job for ASM using the ‘asr’ mode. Everything worked well upto this point. I am seeing at the sample has been processing this step since the past 11+ hours. Do you have an estimate or idea of how long the ASM step would take to run on the size of a VCF and bam file (WGBS) below ?? The log file does not show any error, it only shows “Loading htSNPs ..." And nothing after.
number of Variants in WGBS VCF file = 32,844,420
number of reads in bam file = 59,505,823
For reference, this is a bam file subsetted only to only chromosome X and I am using a powerful compute node using SLURM with 10G of memory to compute the ASM step.
Previously I ran the ASM step on my sample using only 300 SNVs as a test and job completed in roughly 16 minutes. Can you please provide an rough estimate of the time it would take ? I am wondering if something is wrong or its just taking long. I am not seeing any output file generated yet.
Your insight will be very helpful.