A problem occured run smn_caller.py

[dongdongyaa]

hello!!
When I run "smn_caller.py --manifest depth_calling/tests/test_data/NA12885.bam --genome 19 --prefix NA12885 --outDir ./ --threads 2",the error
" File "/public/home/donglijie/miniconda3/envs/smncnv/lib/python3.7/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte"happed.
I wonder how to solve it. Thanks a lot!

[bw2]

The --manifest arg should be a text file. You should try running

echo depth_calling/tests/test_data/NA12885.bam > manifest.txt
python3 smn_caller.py --manifest manifest.txt --genome 19 --prefix NA12885 --outDir ./ --threads 2

[dongdongyaa]

thanks for your reply. I have fixed the error,but another error occured.It's about "ValueError: invalid contig chr5" .When I run my data,the error is TypeError: unsupported operand type(s) for /: 'NoneType' and 'int

[bw2]

"invalid contig" may indicate a mismatch between the reference genome and read data file.
If you post the full python stack trace along with the error message, it may help with troubleshooting.

[dongdongyaa]

I run my bam data,the error like this "INFO:root:Processing sample at 2024-01-30 10:34:34.101195 /public/home/dd/miniconda3/envs/smncnv/bin/depth_calling/bin_count.py:85: RuntimeWarning: divide by zero encountered in true_divide
y_counts = y_counts / np.median(y_counts)
/public/home/dd/miniconda3/envs/smncnv/bin/depth_calling/bin_count.py:85: RuntimeWarning: invalid value encountered in true_divide
y_counts = y_counts / np.median(y_counts)
/public/home/dd/miniconda3/envs/smncnv/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3441: RuntimeWarning: Mean of empty slice.
out=out, **kwargs)
/public/home/dd/miniconda3/envs/smncnv/lib/python3.7/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/public/home/dd/miniconda3/envs/smncnv/bin/depth_calling/bin_count.py:77: RuntimeWarning: divide by zero encountered in true_divide
y_counts = y_counts / np.median(y_counts)
/public/home/dd/miniconda3/envs/smncnv/bin/depth_calling/bin_count.py:77: RuntimeWarning: invalid value encountered in true_divide
y_counts = y_counts / np.median(y_counts)
Traceback (most recent call last):
File "/public/home/dd/miniconda3/envs/smncnv/bin/smn_caller.py", line 298, in
main()
File "/public/home/dd/miniconda3/envs/smncnv/bin/smn_caller.py", line 275, in main
reference_fasta,
File "/public/home/dd/miniconda3/envs/smncnv/bin/smn_caller.py", line 118, in smn_cn_caller
gcall_exon16 = gmm_exon16.gmm_call(normalized_depth.normalized["exon16"])
File "/public/home/dd/miniconda3/envs/smncnv/bin/depth_calling/gmm.py", line 95, in gmm_call
val_new = (val / 2) / self.value_shift
TypeError: unsupported operand type(s) for /: 'NoneType' and 'int'"

[bw2]

I'm not 100% sure, but this error may be due to zero coverage at SMN positions where the tool is expecting reads.

I would open the input bam file in IGV and manually look at these positions on chr5 to make sure there are reads there:
https://github.com/Illumina/SMNCopyNumberCaller/blob/master/data/SMN_SNP_38.txt#L8-L16

Alternatively, you could edit

/public/home/dd/miniconda3/envs/smncnv/bin/depth_calling/bin_count.py

and add some print statements that could give you a better idea of the underlying issue.

[dongdongyaa]

Thanks your helpful advise. My data is targeted sequencing for specific genes,including SMN1.Is this related to reporting errors?

[bw2]

Yes. SMNCopyNumberCaller only works for WGS data because it looks at reads within both exonic and intronic regions of SMN. For targeted sequencing data, you can use https://github.com/broadinstitute/sma_finder (though it only determines whether an individual has SMA ie. affected/unaffected status, and does not report carrier status or SMN1/SMN2 copy number).