Thapeachydude

I've tried running the 2.5 image, but had this error (2.0 works fine). ``` File "/opt/souporcell/souporcell_pipeline.py", line 584, in final_vcf = freebayes(args, bam, fasta) File "/opt/souporcell/souporcell_pipeline.py", line 385, in freebayes...

Hi thanks for the quick response! we've done a test run with 3 samples to see how we are doing, when trying to demultiplex them with bulk WES. I ran...

Thanks for the quick reply! Sure, cluster, retag and minimap error files attached. [errors.zip](https://github.com/wheaton5/souporcell/files/11070045/errors.zip)

Hi again, I've done a bit of digging and saw that a similar issue was reported before (https://github.com/wheaton5/souporcell/issues/137). ``` total loci used 20108 thread '' panicked at 'no entry found...

Thanks for the reply(s)! I ran the whole thing with ``` singularity exec -B /analysis/:/main /resources/software/souporcell_latest.sif souporcell_pipeline.py --clusters 3 --threads 20 --known_genotypes /main/data/vcf/final_wes_2mm.vcf --known_genotypes_sample_names WES_S3 WES_S2 WES_S1 ``` where `main/data/vcf/final_wes_2mm.vcf...

Ok, but in this case how will I be able to map cells to samples in the end?

Hi, so a brief update from my side. I think I made it work (or at least not crash) by removing all variants with phased genotypes e.g. `0|1`. Will try...

Sure. It's quite long, so if there is anything specific you want to see let me know. Also happy to provide plots. ``` ## Input is a seurat object created...

Hi, the first few lines look like this: ``` chr11 207185 G A 1 0.0 0.0 1.0 0.0 NA None 0.0 None None None None -0.38 0.0 chr11 208001 C...