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Dear friend,

ClassifyCNV is so great. I haved tried this excellent software, and get what I want. Here, I have a question refers to the output file. I cannot find the meaning of this column after the column 'Total score', can you add some information about the every column of the output file? Thanks very much.

VariantID
Chromosome
Start
End
Type
Classification
Total score
1 what's the meaning of this column?
2A
2B......................

Dear ClassifyCNV team members,

I am currently trying to annotate a set of 550'000 CNVs using ClassifyCNV. However, the analysis fails with the following error message:

Traceback (most recent call last):
  File "/media/analyst/Data/Scripts/ClassifyCNV-master/ClassifyCNV.py", line 834, in <module>
    analyze_pop_freqs()
  File "/media/analyst/Data/Scripts/ClassifyCNV-master/ClassifyCNV.py", line 737, in analyze_pop_freqs
    overlap_perc = int(fields[9]) * 100 / (int(fields[2]) - int(fields[1]))
ZeroDivisionError: division by zero

I double-checked the file for duplicate rows (same CHR, START, and END), but pandas reports no duplicates. Do you have any idea as to what may be going on?

I just tried running ClassifyCNV on a test bed file but get an error related to the output directory..This occurs whether I specify a path and file name after --outdir or just leave it blank without adding a flag...Is this a bug, or am I entering something wrong? Thanks.

COMMAND LINE:
python3 ClassifyCNV.py --infile XYZ.bed --GenomeBuild hg19 --outdir OUT_TEST

ERROR:
Traceback (most recent call last):
File "ClassifyCNV.py", line 25, in
parser.add_argument('--outdir', default=default_results_folder,
NameError: name 'default_results_folder' is not defined

When I run ClassifyCNV.py, I get
"File "/gpfs52/data/ruderferlab/sandbox/tucker/Scripts/ClassifyCNV/ClassifyCNV.py", line 737, in analyze_pop_freqs
overlap_perc = int(fields[9]) * 100 / (int(fields[2]) - int(fields[1]))
ZeroDivisionError: division by zero"
I inputted a bedfile and I am not sure how to interpret this error in the context of the code.

Your help would be seriously appreciated. Thanks!

Hi,

I am trying to evaluate the following CNV (hg38):
chr16 34963121 36048843 DUP

I ran the update_clingen.sh script and I am using the latest ClassifyCNV version (1.1.0)

However, the script crashes with this error message:

ClassifyCNV-1.1.0/ClassifyCNV.py Version 1.1.0
Traceback (most recent call last):
  File "ClassifyCNV-1.1.0/ClassifyCNV.py", line 817, in <module>
    dosage_sensitivity()
  File "ClassifyCNV-1.1.0/ClassifyCNV.py", line 657, in dosage_sensitivity
    assign_dup_points_s2(dosage_res_dup)
  File "ClassifyCNV-1.1.0/ClassifyCNV.py", line 462, in assign_dup_points_s2
    for gene in cnv_genes[cnv]:
KeyError: 'chr16_34963121_36048843_DUP'

Best,
Tomas

Both hg19 and hg38 versions of the 'ClinGen_triplosensitivity_gene.bed' file miss the 5th column on line 533 (ERCC3 gene) causing a crash. (Easily fixable by either removing the line or adding the 5th column )

Exmaple: line from the hg19 version:
chr2 128014865 128051752 ERCC3

I keep getting this error. I am not sure if its my CNV bedfile.

***** ERROR: illegal number "4.2e+07". Exiting...

***** ERROR: illegal number "4.2e+07". Exiting...

ERROR when running BEDTools on promoters

Good day,
I have been trying to run ClassifyCNV and have had the following error.
Traceback (most recent call last):
File "ClassifyCNV.py", line 834, in
analyze_pop_freqs()
File "ClassifyCNV.py", line 737, in analyze_pop_freqs
overlap_perc = int(fields[9]) * 100 / (int(fields[2]) - int(fields[1]))
ZeroDivisionError: division by zero
I used this command python3 ClassifyCNV.py --infile MTDDgene.bed --GenomeBuild hg38 and here is the beginning of the bed file.

chr1 1339884 1339884 DUP 78
chr1 1450954 1516361 DUP 65407
chr1 1478376 1517082 DUP 38706
chr1 1484927 1522741 DUP 37814
chr1 1529887 1529962 DEL 75
chr1 1530531 1530850 DEL 319
chr1 1532785 1532785 DUP 54
chr1 1842391 1848340 DEL 5949
chr1 2230766 2231750 DEL 984
chr1 2309634 2309829 DEL 195
chr1 3848063 3848421 DEL 358
chr1 5868308 5868634 DEL 314
chr1 5959500 5959580 DEL 80

Could you please assist me is resolving this?
Thank you so much
Regards
Emma

Hi, I try the params of ClassifyCNV.py, The '--cores' param have not useful for speeding up analysis program.
I set '--cores' with 1,2,4,8,16, but the effect is not obvious, now I put the test data below:

What should I do, If I fail to correctly use ClassifyCNV.py "--cores", please tell me what I error. Thanks.

Hi,
I haved tried ClassifyCNV recently, and this is a excellent software. Here, I wonder how the population frequencies database (population_freqs.bed file) was obtained. Does it integrated from DGV and gnomAD?
Thanks very much.

Best，
Niki

Hello, when I used classifyCNV on my data, it ran normally but I checked the number of variants and they were less than the input. There wasn't any errors when I ran the tool so I didn't know why there was missing output.

Hi, I tried to run ClassifyCNV by Python3 from my Linux terminal, but the output told me that it was an error in position 4 with a decode byte 0xa8. I searched it in the web but I can't solve this problem. Could you assist me with this?