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.