ZeroDivisionError: division by zero

[waterhouseBenth]

Hello,

I got error below. is it the error caused by small number of K-mer? how to change options to avoid the error?

Thanks
anji

...
25-03-21 16:16:24 [INFO] 45488711 kmers in total
25-03-21 16:16:24 [INFO] Filtering differential kmers
25-03-21 16:16:24 [WARNING] Singleton [['09']] is ignored
25-03-21 16:16:24 [WARNING] Singleton [['10']] is ignored
25-03-21 16:16:24 [WARNING] Singleton [['19']] is ignored
25-03-21 16:16:27 [INFO] Start Pool with 16 process(es)
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/Jellyfish.py", line 629, in _filter_kmer
freq = count/lens if not by_count else count
ZeroDivisionError: division by zero
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/an/miniconda3/envs/SubPhaser/bin/subphaser", line 33, in
sys.exit(load_entry_point('subphaser==1.2.6', 'console_scripts', 'subphaser')())
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/main.py", line 797, in main
pipeline.run()
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/main.py", line 422, in run
d_mat = dumps.filter(d_mat, lengths, self.sgs, outfig=histfig, #d_targets=d_targets,
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/Jellyfish.py", line 491, in filter
for kmer, freqs, tot_freq in pool_func(_filter_kmer, args, self.ncpu,
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/RunCmdsMP.py", line 347, in pool_func
for returned in pool_map(func, iterable, **kargs):
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/an/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
ZeroDivisionError: division by zero

[zhangrengang]

Hi @waterhouseBenth . This error likely occurs because the kmer count for one or more chromosomes is zero, which prevents the calculation of proportions. Please check the input and intermediate files. I have added a line of code to output a log indicating which chromosome has a count of zero, which you can try.

[waterhouseBenth]

thanks, I am going to download new version.
I have another question I generated config file as below. because chr07, chr08 and chr09 do not have homo-chromosome, I add them in one line. In the result folder, I found in the circos plot, chr07 and chr08 are missing. my question is that can we have more than one non-paired chromosomes?
1|chr01 2|chr02
2|chr03 3|chr04
3|chr05 4|chr06
7|chr07
8|chr08
9|chr09

[zhangrengang]

The answer is yes. You need to check the intermediate files to find out when and why the two chrs are missing.

[waterhouseBenth]

thanks, how about one chrom appears in two rows?
1|chr01 2|chr02
2|chr01 3|chr03

[zhangrengang]

It is allowed, but 2|chr01 should be 1|chr01.