ZeroDivisionError in the nonnormal mode

[kzb193]

Hello,

I am trying to apply chisel_nonormal on a 10x scDNAseq data. But, I am getting a long sequence of error messages that appears to be similar. Can you please help me with this?

Specifically, I have applied the following steps.

1) used full automatic installation, and completed the quick start check. 2) called snps from the tumor bam as bcftools mpileup --ignore-RG --threads 10 -f $REF $BAM | bcftools call -mv -Oz -o $F_OUT 3) used eagle2 for phasing based on 1000 Genomes Phase 3 panel, and there are 1344782 many phased het. snps distributed across chr 1-22 in the resulting vcf file. 4) called chisel as chisel_nonormal -t ${TUM} -r ${REF} -l ${PHA} --seed 12

An empty bcf.tsv file is generated along with a log file which is attached here as baf_log.txt baf_log.txt Additionally, the log file generated in the 'rdr' folder is attached here as rdr_log.txt rdr_log.txt

A portion from the flow of error messages

Traceback (most recent call last): File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, *self._kwargs) File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/multiprocessing/pool.py", line 97, in worker initializer(initargs) File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/site-packages/chisel/Combiner.py", line 234, in init alpha_correct = args['significance'] / (20 float(sum(len(snps[c]) for c in snps))) ZeroDivisionError: float division by zero Process PoolWorker-4233311: Traceback (most recent call last): File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(self._args, *self._kwargs) File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/multiprocessing/pool.py", line 97, in worker initializer(initargs) File "/net/mulan/home/kalinsba/apps/chisel/conda/envs/chisel/lib/python2.7/site-packages/chisel/Combiner.py", line 234, in init alpha_correct = args['significance'] / (20 * float(sum(len(snps[c]) for c in snps))) ....................................................................

Please let me know if you need any other details. Thank you!

[kzb193]

Hello,

Can you please help me out on this issue?

Thanks.