SMNCOPYNUMBERCALLER ZeroDivisionError: float division by zero

[yunhua1031]

Description of the bug

Hello, I've got the basic test run to work, and now I'm trying the pipeline on real data, which I have trouble to get the pipeline to work... I got error at SMNCOPYNUMBERCALLER step:

... Caused by: Process NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) terminated with an error exit status (1)

Command executed:

echo earlycasualcaiman_sorted_md.bam slowlycivilbuck_sorted_md.bam hugelymodelbat_sorted_md.bam | tr ' ' ' ' > manifest.txt smn_caller.py
--genome 38
--manifest manifest.txt
--prefix justhusky
--outDir "out"
--threads 2

cat <<-END_VERSIONS > versions.yml "NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER": SMNCopyNumberCaller: 1.1.2 END_VERSIONS

Command exit status: 1

Command output: (empty)

Command error: INFO:root:Processing sample earlycasualcaiman_sorted_md at 2023-11-20 23:57:42.498223 /usr/local/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3432: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /usr/local/lib/python3.10/site-packages/numpy/core/_methods.py:190: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) /usr/local/bin/depth_calling/bin_count.py:85: RuntimeWarning: divide by zero encountered in divide y_counts = y_counts / np.median(y_counts) /usr/local/bin/depth_calling/bin_count.py:85: RuntimeWarning: invalid value encountered in divide y_counts = y_counts / np.median(y_counts) /usr/local/bin/depth_calling/bin_count.py:77: RuntimeWarning: divide by zero encountered in divide y_counts = y_counts / np.median(y_counts) /usr/local/bin/depth_calling/bin_count.py:77: RuntimeWarning: invalid value encountered in divide y_counts = y_counts / np.median(y_counts) Traceback (most recent call last): File "/usr/local/bin/smn_caller.py", line 298, in main() File "/usr/local/bin/smn_caller.py", line 267, in main smn_call = smn_cn_caller( File "/usr/local/bin/smn_caller.py", line 118, in smn_cn_caller gcall_exon16 = gmm_exon16.gmm_call(normalized_depth.normalized["exon16"]) File "/usr/local/bin/depth_calling/gmm.py", line 96, in gmm_call fcall = self.call_post_prob(val_new, POSTERIOR_CUTOFF) File "/usr/local/bin/depth_calling/gmm.py", line 125, in call_post_prob post_prob = [float(a) / sum_prob for a in prob] File "/usr/local/bin/depth_calling/gmm.py", line 125, in post_prob = [float(a) / sum_prob for a in prob] ZeroDivisionError: float division by zero

variant_catalog_hg38_TEST.json wholegenome.interval_list.txt chrY.interval_list.txt

Command used and terminal output

$ cat nf-params.json
{
    "input": "samplesheet.csv",
    "outdir": "RD_Results",
    "save_reference": true,
    "genome": "GRCh38",
    "intervals_wgs": "wholegenome.interval_list.txt",
    "intervals_y" : "chrY.interval_list.txt",
    "target_bed" : "GRCh38.p14.bed",
    "variant_catalog" : "variant_catalog_hg38_TEST.json",
    "skip_cnv_calling": true,
    "skip_mt_analysis": true,
    "skip_snv_annotation": true,
    "skip_sv_annotation": true,
    "variant_type": "snp,indel"
}

$ cat samplesheet.csv
sample,single_end,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id
earlycasualcaiman_T1,False,1,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz,1,1,0,0,justhusky
slowlycivilbuck_T1,False,1,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,2,1,0,0,justhusky
hugelymodelbat_T1,False,1,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz,1,2,earlycasualcaiman,slowlycivilbuck,justhusky

$ cat GRCh38.p14.bed
chr1    0       248956422
chr2    0       242193529
chr3    0       198295559
chr4    0       190214555
chr5    0       181538259
chr6    0       170805979
chr7    0       159345973
chr8    0       145138636
chr9    0       138394717
chr10   0       133797422
chr11   0       135086622
chr12   0       133275309
chr13   0       114364328
chr14   0       107043718
chr15   0       101991189
chr16   0       90338345
chr17   0       83257441
chr18   0       80373285
chr19   0       58617616
chr20   0       64444167
chr21   0       46709983
chr22   0       50818468
chrX    0       156040895
chrY    0       57227415

$ nohup nextflow run nf-core/raredisease -r 1.1.1 -profile docker -params-file nf-params.json

Relevant files

No response

System information

N E X T F L O W ~ version 23.10.0 Hardware: HPC OS: CentOS nf-core/raredisease: 1.1.1

[ramprasadn]

Can you share the fasta file you used for this run somehow?

[yunhua1031]

Hi @ramprasadn, I was using the iGenome reference, so I didn't input a fasta file.

[yunhua1031]

Hi @ramprasadn, just want to follow up :) Any insight?

[ramprasadn]

Hi @yunhua1031! Sorry I have been on vacation, and just catching up with pending tasks. Could you run smncopynumbercaller outside of the pipeline with the same input file and see if the error persists?