Circle_Map takes an unusually long time to read files.

[ghost]

I'm sorry to bother you, but I had a strange problem when using circle-map for EccDNA identification. I have a total of 14 samples, of which 12 samples were identified very quickly and finished in about 1.5 hour. But the other two samples are particularly slow and have been running for four days with no results.

[EvAnhaodong]

I found the reason is that the depth of some region is too high.
The codes where the exception occurs is in circlemap/utils.py line 1204,1208,1219,1222.
pysam's function bam.count() will take a lot of time if the position depth is too high. The problem will also occur in samtools view -c .
I think you can use the -S parameter to increase the threshold and speed up.
But the best way is to adjust the filtering strategy of candidate eccDNA in circlemap/utils.py line 1203 @iprada