PeterSu92

No, just on my local machine, which is a windows but I'm running it on WSL. Do I need to change the allocation? I remember reading about that somewhere..

Hmm what happens if I set the genome size to 2Gb instead of the 3.2Gb, in terms of how the algorithm works?

Looks like it was able to run the job, any way to tell if it did anything super awry? [2023-08-15 22:34:19] =============Start==================== [2023-08-15 22:34:31] Bad quality threshold is "D" [2023-08-15...

Oh, I purposefully used a subset of reads to troubleshoot code so that it wouldn't take forever since I was just trying to play around. In theory though, it should've...

Alright I tried it on the full dataset and it gave the signal 9 error again. So do you think I just need more RAM then?

Here's the output of $ grep "^##" -v T2T_combined_output.vcf | head -n 10 (sorry the formatting sucks) ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT psu_dna_fwd CP068277.2 5546...

Ah ok thanks, will do that and try again

Ok great, the first few lines of my VCF files (excluding the headers) now look like this: `1 116723 . C T 36.65 . AC=1;AF=0.5;AN=2;BaseQRankSum=-0.431;DP=3;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=22;MQRankSum=0;QD=12.22;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:18:44,0,18 1 116962 ....