Hi,
When I follow the tutorial for identification of circular DNA using Circle Map Realign,I encounter an error.
My command Input:Circle-Map Realign -i 019_sort_circular_read_candidates.bam -qbam 019_qname.bam -sbam 019_sort.bam -fasta 019_new.fna -o 019_circle.bedThe standard output gives an error:
2020-09-03 09:08:43: Realigning reads using Circle-Map
2020-09-03 09:08:43: Clustering structural variant reads
2020-09-03 09:08:44: Splitting clusters to to processors
[E::idx_find_and_load] Could not retrieve index file for '019_qname.bam'
0%| Traceback (most recent call last): | 0/100 [00:00<?, ?it/s]
File "/beegfs/home/lxd/miniconda3/envs/pgcgap/lib/python3.7/site-packages/circlemap/realigner.py", line 222, in realign
plus_base_freqs = background_freqs(plus_coding_interval)
File "/beegfs/home/lxd/miniconda3/envs/pgcgap/lib/python3.7/site-packages/circlemap/utils.py", line 876, in background_freqs
return{nucleotide: seq.count(nucleotide)/len(seq) for nucleotide in 'ATCG'}
File "/beegfs/home/lxd/miniconda3/envs/pgcgap/lib/python3.7/site-packages/circlemap/utils.py", line 876, in <dictcomp>
return{nucleotide: seq.count(nucleotide)/len(seq) for nucleotide in 'ATCG'}
ZeroDivisionError: division by zero
/beegfs/home/lxd/miniconda3/envs/pgcgap/lib/python3.7/site-packages/circlemap/realigner.py:391: UserWarning: Failed on interval chrom 019_contig161
start 25534
end 25834
Name: 2, dtype: object due to the error division by zero
str(interval), str(e)))
1%|█▎ | 1/100 [00:01<02:59, 1.81s/it]
2020-09-03 09:08:46: An error happenend during execution. Exiting
0it [00:01, ?it/s]
Hi, When I follow the tutorial for identification of circular DNA using Circle Map Realign,I encounter an error. My command Input:
Circle-Map Realign -i 019_sort_circular_read_candidates.bam -qbam 019_qname.bam -sbam 019_sort.bam -fasta 019_new.fna -o 019_circle.bed
The standard output gives an error:Thanks a lot, hope to get your suggestions!