Zero division error

[AishaAJ]

I'm getting this error.

[bam_sort_core] merging from 5 files... [06/21 03:20:52PM][INFO][alignReads] Sorting for control_U2OS_EMX1_rep_1 by name complete. [06/21 03:20:52PM][INFO][circleseq] Finished merging and aligning reads. [06/21 03:20:52PM][INFO][circleseq] Identifying off-target cleavage sites. [06/21 03:20:52PM][INFO][circleseq] Reads: 4, Window: 3, MAPQ: 50, Gap: 3, Start 1, Mismatches 6 Writing counts to ./identified/U2OS_EMX1_rep_3_count.txt Tabulate nuclease merged start positions. 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 8.9 9.0 9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 9.9 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 10.8 10.9 11.0 11.1 11.2 11.3 11.4 11.5 11.6 11.7 11.8 11.9 12.0 12.1 12.2 12.3 12.4 12.5 12.6 12.7 12.8 12.9 13.0 13.1 13.2 Tabulate control merged start positions. 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0 3.1 3.2 3.3 3.4 3.5 [06/21 03:35:04PM][ERROR][circleseq] Error identifying off-target cleavage site. [06/21 03:35:04PM][ERROR][circleseq] Traceback (most recent call last): File "circleseq/circleseq/circleseq.py", line 157, in findCleavageSites identified_sites_file, merged=self.merged_analysis) File "/Users/aljanahiaa/runs/circleseq/circleseq/circleseq/findCleavageSites.py", line 577, in compare ecdf_pos = statsmodels.distributions.empirical_distribution.ECDF(bg_position) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/statsmodels/distributions/empirical_distribution.py", line 140, in init y = np.linspace(1./nobs,1,nobs) ZeroDivisionError: float division by zero

[AishaAJ]

Renaming my chromosomes to "1, 2, 3....X" fixed this.

[shengdar]

Now all chromosome format names are supported.

[Akitsu505]

I am trying to run circleseq.py (downloaded on June 2018), but still getting the same error as above. My reference hg38 and mapped sam/bam files use chr1, chr2, ...chrX, instead of 1, 2, ...X. Should I change all the chromosome names on bam/sam files? Please let me know how the chromosome format names are supported.

Thanks for developing the nice tool, by the way.

[07/19 02:03:24PM][INFO][alignReads] Sorting for control_1383D2_CS02_Alu by name complete. [07/19 02:03:24PM][INFO][circleseq] Finished merging and aligning reads. [07/19 02:03:24PM][INFO][circleseq] Identifying off-target cleavage sites. [07/19 02:03:24PM][INFO][circleseq] Window: 3, MAPQ: 50, Gap: 3, Start 1, Mismatches 6, Search_Radius 20 Writing counts to ./Experimental_data/180717_CIRCLE-seq-analysis/identified/1383D2_CS02_Alu_count.txt Tabulate nuclease merged start positions. 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0ATabulate control merged start positions. 0.1A0.2A0.3A0.4A0.5A0.6A0.7A0.8A0.9A1.0A1.1A1.2A1.3A1.4A1.5A1.6A1.7A1.8A1.9A2.0A2.1A2.2A2.3A2.4A2.5A2.6A2.7A2.8A2.9A3.0A3.1A3.2A3.3A3.4A3.5A3.663.76[]A[] [07/19 02:05:38PM][ERROR][circleseq] Error identifying off-target cleavage site. [07/19 02:05:38PM][ERROR][circleseq] Traceback (most recent call last): File "./circleseq/circleseq/circleseq.py", line 168, in findCleavageSites identified_sites_file, self.all_chromosomes, merged=self.merged_analysis) File "./circleseq/circleseq/findCleavageSites.py", line 611, in compare ecdf_pos = ECDF(bg_position) File "/anaconda2/lib/python2.7/site-packages/statsmodels/distributions/empirical_distribution.py", line 140, in init y = np.linspace(1./nobs,1,nobs) ZeroDivisionError: float division by zero