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It is a great work for developing sicer2.
I get some bug when using sicer2.I add a new spesis of tair10 and use sicer2 to call different peak region. The bed files came from macs2 H3ac_col0_peaks.bed.txt and H3ac_hda6_peaks.bed.txt.
Running SICER with given arguments
Preprocess the H3ac_col0_peaks.bed file to remove redundancy with threshold of 1
---------------------------------------------------------------------------------------------------------
chrom Total plus reads Retained plus reads Total minus reads Retained minus reads
---------------------------------------------------------------------------------------------------------
1 0 0 10150 10150
2 0 0 8752 8752
3 0 0 9282 9282
4 0 0 8739 8739
5 0 0 9857 9857
Mt 0 0 47 47
Pt 0 0 40 40
Partition the genome in windows and generate summary files...
Total count of 1 tags: 0
Total count of 1 tags: 0
Total count of 1 tags: 0
Total count of 1 tags: 0
Total count of 1 tags: 0
Total count of Mt tags: 0
Total count of Pt tags: 0
Normalizing graphs by total island filitered reads per million and generating summary WIG file...
Finding candidate islands exhibiting clustering...
Species: tair10
Window_size: 200
Gap size: 600
E value is: 1000
Total read count: 0
Genome Length: 119667750
Effective genome Length: 88554135
Window average: 0.0
Traceback (most recent call last):
File "/home/xiaoming/conda/miniconda3/envs/chipseq/bin/sicer_df", line 7, in <module>
exec(compile(f.read(), __file__, 'exec'))
File "/share/xiaoming/github_software/SICER2/bin/sicer_df", line 254, in <module>
main()
File "/share/xiaoming/github_software/SICER2/bin/sicer_df", line 249, in main
run_SICER_df.main(args)
File "/share/xiaoming/github_software/SICER2/sicer/main/run_SICER_df.py", line 43, in main
temp_dir_1, library_size_file1 = run_SICER.main(args_1, True)
File "/share/xiaoming/github_software/SICER2/sicer/main/run_SICER.py", line 77, in main
find_islands_in_pr.main(args, total_tag_in_windows, pool)
File "/share/xiaoming/github_software/SICER2/sicer/src/find_islands_in_pr.py", line 171, in main
background = Background_island_probscore_statistics.Background_island_probscore_statistics(total_read_count,
File "/share/xiaoming/github_software/SICER2/sicer/lib/Background_island_probscore_statistics.py", line 41, in __init__
prob = self.poisson(index, self.average);
File "/share/xiaoming/github_software/SICER2/sicer/lib/Background_island_probscore_statistics.py", line 121, in poisson
exponent = -average + i * log(average) - self.factln(i)
ValueError: math domain error
The text was updated successfully, but these errors were encountered:
It is a great work for developing sicer2.
I get some bug when using sicer2.I add a new spesis of tair10 and use sicer2 to call different peak region. The bed files came from macs2
H3ac_col0_peaks.bed.txt and H3ac_hda6_peaks.bed.txt.
the bug report laid below
The text was updated successfully, but these errors were encountered: