ValueError: zero-size array to reduction operation minimum which has no identity

[olegs]

I try to call peaks using Fseq2, but it fails with a runtime error.
The command line:
fseq2 callpeak -v -cpus 1 -q_thr 0.05 -control_file bams/pileup/CD34_Control_hg38_ENCFF112IIL.filtered.bed -chrom_size_file hg38.chrom.sizes -o fseq2 -name CD34_H3K36me3_rep1_hg38_ENCFF785IJG -standard_narrowpeak bams/pileup/CD34_H3K36me3_rep1_hg38_ENCFF785IJG.filtered.bed

PROGRAM: fseq2.0.3 callpeak
=====================================
F-Seq Version 2.0.3
=====================================
#1: Read in files and calculate parameters
#1: Done
#1: Settings:

        bandwidth = 100.000
        threshold = 5.288
        lambda bg lower bound = 0.022
        est. fragment size = 150
        sequence length = 36
        total cuts = 7489277

        control bandwidth = 2000.000
        control est. fragment size = 152
        control sequence length = 36
        control total cuts = 16065200

-------------------------------------
#2: Reconstruct signal and call peaks

        chr10: first=13765, last=133787088, completed in 37.830 seconds.
        chr11: first=70736, last=135076123, completed in 37.686 seconds.
no peaks found on chr11_KI270721v1_random
        chr12: first=11814, last=133263270, completed in 38.509 seconds.
        chr13: first=16000439, last=114353974, completed in 27.594 seconds.
        chr14: first=16022901, last=106883396, completed in 25.251 seconds.
no peaks found on chr14_GL000009v2_random
        chr14_GL000194v1_random: first=2404, last=190128, completed in 0.038 seconds.
        chr14_GL000225v1_random: first=19, last=206891, completed in 0.045 seconds.
        chr14_KI270722v1_random: first=305, last=193849, completed in 0.038 seconds.
no peaks found on chr14_KI270723v1_random
no peaks found on chr14_KI270724v1_random
        chr14_KI270725v1_random: first=7201, last=172739, completed in 0.080 seconds.
no peaks found on chr14_KI270726v1_random
        chr15: first=17009846, last=101980758, completed in 23.882 seconds.
no peaks found on chr15_KI270727v1_random
        chr16: first=17079, last=90222598, completed in 25.588 seconds.
no peaks found on chr16_KI270728v1_random
        chr17: first=73025, last=83245366, completed in 23.594 seconds.
        chr17_GL000205v2_random: first=101, last=184498, completed in 0.040 seconds.
        chr17_KI270729v1_random: first=11, last=280491, completed in 0.055 seconds.
        chr17_KI270730v1_random: first=7263, last=112473, completed in 0.028 seconds.
        chr18: first=35797, last=80261840, completed in 22.870 seconds.
        chr19: first=72753, last=58604982, completed in 15.577 seconds.
no peaks found on chr1_KI270706v1_random
no peaks found on chr1_KI270707v1_random
no peaks found on chr1_KI270708v1_random
        chr1_KI270709v1_random: first=443, last=66210, completed in 0.054 seconds.
no peaks found on chr1_KI270710v1_random
        chr1_KI270711v1_random: first=5939, last=41252, completed in 0.019 seconds.
no peaks found on chr1_KI270712v1_random
no peaks found on chr1_KI270713v1_random
no peaks found on chr1_KI270714v1_random
        chr20: first=60154, last=64333678, completed in 17.110 seconds.
        chr21: first=5030705, last=46689620, completed in 11.311 seconds.
        chr22: first=10531757, last=50807842, completed in 10.941 seconds.
no peaks found on chr22_KI270731v1_random
no peaks found on chr22_KI270732v1_random
        chr22_KI270733v1_random: first=50, last=173248, completed in 0.038 seconds.
no peaks found on chr22_KI270734v1_random
        chr22_KI270735v1_random: first=249, last=42654, completed in 0.019 seconds.
        chr22_KI270736v1_random: first=545, last=181816, completed in 0.039 seconds.
no peaks found on chr22_KI270737v1_random
        chr22_KI270738v1_random: first=188, last=98647, completed in 0.062 seconds.
no peaks found on chr22_KI270739v1_random
no peaks found on chr2_KI270715v1_random
        chr2_KI270716v1_random: first=145, last=129298, completed in 0.030 seconds.
no peaks found on chr3_GL000221v1_random
        chr4_GL000008v2_random: first=9, last=208174, completed in 0.041 seconds.
        chr5_GL000208v1_random: first=376, last=89409, completed in 0.025 seconds.
no peaks found on chr9_KI270717v1_random
no peaks found on chr9_KI270718v1_random
        chr9_KI270719v1_random: first=551, last=176425, completed in 0.038 seconds.
no peaks found on chr9_KI270720v1_random
multiprocessing.pool.RemoteTraceback:
Traceback (most recent call last):
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/multiprocessing/pool.py", line 51, in starmapstar
    return list(itertools.starmap(args[0], args[1]))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/site-packages/fseq2/fseq2.py", line 225, in run_kde
    kdepy_result_control, first_cut_control, _ = calculate_kde(cuts_array=cuts_array_control,
                                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/site-packages/fseq2/fseq2.py", line 405, in calculate_kde
    first_cut = np.min(cuts_array)
                ^^^^^^^^^^^^^^^^^^
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/site-packages/numpy/core/fromnumeric.py", line 2953, in min
    return _wrapreduction(a, np.minimum, 'min', axis, None, out,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/site-packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no identity
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/bin/fseq2", line 441, in <module>
    main(temp_dir_name)
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/bin/fseq2", line 50, in main
    submain(args)
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/site-packages/fseq2/callpeak_main.py", line 181, in main
    results = pool.starmap(fseq2.run_kde, input_param_ls)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/multiprocessing/pool.py", line 375, in starmap
    return self._map_async(func, iterable, starmapstar, chunksize).get()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jetbrains/data/2023_Immune/.snakemake/conda/173f449360086db0b415b579adf49e14_/lib/python3.12/multiprocessing/pool.py", line 774, in get
    raise self._value
ValueError: zero-size array to reduction operation minimum which has no identity

[LinearParadox]

I've had this in the past, and what I believe happens is that the decoy chromosomes like " chr5_GL000208v1_random" have no cuts on there respective arrays, and therefore when numpy tries to take the min of an empty array an error is thrown. I generally toss reads that map to unlocalized scaffolds and such. I'm not sure how you would meaningfully interpret them as these are areas that are quite difficult to assemble, and I wouldn't be super confident about peaks in them to begin with.