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ValueError: math domain error #21

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MingLi-929 opened this issue Feb 1, 2023 · 0 comments
Open

ValueError: math domain error #21

MingLi-929 opened this issue Feb 1, 2023 · 0 comments

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@MingLi-929
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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.

sicer_df -t ../callpeak_result/H3ac_col0/H3ac_col0_peaks.bed ../callpeak_result/H3ac_hda6/H3ac_hda6_peaks.bed -s tair10

the bug report laid below

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
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