Error processing cell S0401B: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 2 is required by GaussianMixture.

[zhaoxiaofei]

Hi there,

I have encountered the following error, do you know what might be the cause of such error?
I already asked Claude and did not get a meaningful answer.

(hiscanner_test) zxf@xglab2080ti:/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project$ date ; command time -v hiscanner run --step all ; date
2026年 04月 06日 星期一 10:40:06 CST
INFO     Running complete pipeline...
INFO     Running snp step...
INFO     Preparing SNP calling results
WARNING  Missing Raw variants VCF MD5: /stor/zxf/cnv/cnvguider/scan2/demo/gatk/hc_raw.mmq60.vcf.gz.md5
WARNING  Missing Phased hets VCF MD5: /stor/zxf/cnv/cnvguider/scan2/demo/shapeit/phased_hets.vcf.gz.md5
INFO     SNP calling results prepared successfully
INFO     Running phase step...
INFO     Starting phasing step
WARNING  Missing Raw variants VCF MD5: /stor/zxf/cnv/cnvguider/scan2/demo/gatk/hc_raw.mmq60.vcf.gz.md5
WARNING  Missing Phased hets VCF MD5: /stor/zxf/cnv/cnvguider/scan2/demo/shapeit/phased_hets.vcf.gz.md5
INFO     Processing 3 cells
INFO     Skipping existing results for S0401B
INFO     Skipping existing results for S0401C
INFO     Skipping existing results for S0402A
INFO     Phasing step completed successfully
INFO     Running ado step...
INFO     Starting ADO analysis
INFO     Performing ADO analysis for 3 cells
INFO     Total number of hetSNPs for S0401B: 5928
INFO     Plotting pBAF distribution for S0401B
INFO     Plotting pBAF distribution
INFO     Aggregating every 5 SNPs
INFO     Loading existing data for S0401B
INFO     Suggested minimum bin size (kb): 31485.0
INFO     Total number of hetSNPs for S0401C: 12674
INFO     Plotting pBAF distribution for S0401C
INFO     Plotting pBAF distribution
INFO     Aggregating every 5 SNPs
INFO     Loading existing data for S0401C
INFO     Suggested minimum bin size (kb): 13198.0
INFO     Total number of hetSNPs for S0402A: 11555
INFO     Plotting pBAF distribution for S0402A
INFO     Plotting pBAF distribution
INFO     Aggregating every 5 SNPs
INFO     Loading existing data for S0402A
INFO     Suggested minimum bin size (kb): 13670.0
INFO     ================================================================================
INFO     SUGGESTED BIN SIZE FOR ALL CELLS: at least 31485.0 kb.
INFO     Please edit the bin size in the config file to the suggested value.
INFO     ================================================================================
INFO     ADO analysis completed successfully
INFO     Running normalize step...
INFO     Starting normalization pipeline
INFO     Workflow setup completed in /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/.workflow
INFO     Running normalization workflow from /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/.workflow

WARNING  Snakemake stderr:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job                count
---------------  -------
all                    1
run_bicseq_norm        3
total                  4

Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807}
Ready jobs (3)
Select jobs to execute...
Selected jobs (3)
Resources after job selection: {'_cores': 1, '_nodes': 9223372036854775804}

[Mon Apr  6 10:40:49 2026]
rule run_bicseq_norm:
    input: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0401C.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/1.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/2.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/3.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/4.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/5.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/6.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/7.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/8.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/9.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/10.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/11.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/12.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/13.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/14.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/15.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/16.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/17.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/18.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/19.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/20.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/21.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/22.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/X.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/Y.readpos.seq
    output: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/1.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/2.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/3.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/4.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/5.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/6.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/7.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/8.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/9.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/10.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/11.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/12.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/13.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/14.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/15.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/16.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/17.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/18.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/19.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/20.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/21.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/22.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/X.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/Y.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp/S0401C.temp
    log: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/logs/bicseq_norm_S0401C.log
    jobid: 77
    reason: Params have changed since last execution
    wildcards: sample=S0401C
    resources: tmpdir=/tmp


        mkdir -p /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp
        /nfs/public/zxf/miniconda3/envs/hiscanner_test/lib/python3.8/site-packages/hiscanner/resources/tools/singlesample_norm/NBICseq-norm.pl             -b=5000000             --gc_bin             -p=0.0001             --tmp=/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp             /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0401C.cfg             /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp/S0401C.temp 2> /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/logs/bicseq_norm_S0401C.log
        

[Mon Apr  6 10:40:49 2026]
rule run_bicseq_norm:
    input: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0402A.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/1.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/2.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/3.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/4.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/5.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/6.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/7.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/8.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/9.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/10.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/11.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/12.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/13.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/14.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/15.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/16.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/17.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/18.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/19.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/20.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/21.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/22.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/X.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/Y.readpos.seq
    output: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/1.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/2.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/3.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/4.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/5.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/6.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/7.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/8.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/9.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/10.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/11.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/12.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/13.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/14.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/15.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/16.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/17.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/18.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/19.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/20.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/21.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/22.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/X.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/Y.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp/S0402A.temp
    log: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/logs/bicseq_norm_S0402A.log
    jobid: 78
    reason: Params have changed since last execution
    wildcards: sample=S0402A
    resources: tmpdir=/tmp


        mkdir -p /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp
        /nfs/public/zxf/miniconda3/envs/hiscanner_test/lib/python3.8/site-packages/hiscanner/resources/tools/singlesample_norm/NBICseq-norm.pl             -b=5000000             --gc_bin             -p=0.0001             --tmp=/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp             /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0402A.cfg             /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp/S0402A.temp 2> /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/logs/bicseq_norm_S0402A.log
        

[Mon Apr  6 10:40:49 2026]
rule run_bicseq_norm:
    input: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0401B.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/1.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/2.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/3.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/4.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/5.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/6.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/7.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/8.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/9.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/10.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/11.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/12.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/13.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/14.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/15.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/16.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/17.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/18.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/19.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/20.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/21.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/22.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/X.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/Y.readpos.seq
    output: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/1.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/2.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/3.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/4.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/5.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/6.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/7.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/8.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/9.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/10.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/11.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/12.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/13.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/14.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/15.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/16.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/17.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/18.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/19.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/20.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/21.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/22.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/X.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/Y.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp/S0401B.temp
    log: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/logs/bicseq_norm_S0401B.log
    jobid: 76
    reason: Params have changed since last execution
    wildcards: sample=S0401B
    resources: tmpdir=/tmp


        mkdir -p /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp
        /nfs/public/zxf/miniconda3/envs/hiscanner_test/lib/python3.8/site-packages/hiscanner/resources/tools/singlesample_norm/NBICseq-norm.pl             -b=5000000             --gc_bin             -p=0.0001             --tmp=/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp             /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0401B.cfg             /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/temp/S0401B.temp 2> /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/logs/bicseq_norm_S0401B.log
        
[Mon Apr  6 12:44:09 2026]
Finished job 76.
1 of 4 steps (25%) done
[Mon Apr  6 12:44:24 2026]
Finished job 78.
2 of 4 steps (50%) done
[Mon Apr  6 12:44:28 2026]
Finished job 77.
3 of 4 steps (75%) done
Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807}
Ready jobs (1)
Select jobs to execute...
Selected jobs (1)
Resources after job selection: {'_cores': 3, '_nodes': 9223372036854775806}

[Mon Apr  6 12:44:28 2026]
localrule all:
    input: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0401B.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0401C.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/cfg/S0402A.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/segcfg/S0401B.seg.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/segcfg/S0401C.seg.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/segcfg/S0402A.seg.cfg, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/1.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/2.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/3.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/4.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/5.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/6.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/7.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/8.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/9.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/10.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/11.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/12.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/13.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/14.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/15.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/16.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/17.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/18.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/19.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/20.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/21.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/22.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/X.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401B/Y.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/1.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/2.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/3.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/4.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/5.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/6.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/7.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/8.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/9.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/10.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/11.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/12.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/13.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/14.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/15.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/16.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/17.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/18.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/19.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/20.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/21.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/22.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/X.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0401C/Y.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/1.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/2.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/3.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/4.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/5.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/6.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/7.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/8.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/9.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/10.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/11.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/12.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/13.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/14.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/15.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/16.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/17.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/18.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/19.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/20.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/21.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/22.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/X.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/readpos/S0402A/Y.readpos.seq, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/1.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/2.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/3.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/4.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/5.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/6.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/7.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/8.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/9.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/10.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/11.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/12.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/13.bin, 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/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/16.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/17.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/18.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/19.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/20.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/21.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/22.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/X.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/Y.bin
    jobid: 0
    reason: Input files updated by another job: /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/22.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/X.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/10.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/X.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/Y.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/8.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/13.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/15.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/13.bin, 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/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/X.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/11.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/2.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/4.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/18.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/10.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/20.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/16.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/5.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/12.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/8.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401B/8.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/4.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/5.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/5.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/20.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/13.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/22.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/21.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/3.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0402A/15.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/15.bin, /stor/zxf/cnv/cnvguider/hiscanner_demo/my_project/hiscanner_output_g1k_v37test/bins/S0401C/17.bin
    resources: tmpdir=/tmp

[Mon Apr  6 12:44:28 2026]
Finished job 0.
4 of 4 steps (100%) done
Complete log: .snakemake/log/2026-04-06T104047.007406.snakemake.log

INFO     Normalization pipeline completed successfully
INFO     Running segment step...
INFO     Starting segmentation
INFO     Running single-sample segmentation
INFO     Segmentation completed successfully
INFO     Running cnv step...
INFO     Starting CNV calling pipeline
INFO     Using standard (RDR + BAF) mode
INFO     Saving final calls to hiscanner_output_g1k_v37test/final_calls
INFO     Processing cell S0401B
INFO     Reading segments for S0401B (lambda=16)
INFO     Annotating segments
INFO     Finding allelic balanced clusters
ERROR    Error processing cell S0401B: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 2 is required by GaussianMixture.
ERROR    Error in CNV calling pipeline: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 2 is required by GaussianMixture.
ERROR    Error running pipeline: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 2 is required by GaussianMixture.
Command exited with non-zero status 1
	Command being timed: "hiscanner run --step all"
	User time (seconds): 11030.97
	System time (seconds): 512.82
	Percent of CPU this job got: 154%
	Elapsed (wall clock) time (h:mm:ss or m:ss): 2:04:36
	Average shared text size (kbytes): 0
	Average unshared data size (kbytes): 0
	Average stack size (kbytes): 0
	Average total size (kbytes): 0
	Maximum resident set size (kbytes): 3752580
	Average resident set size (kbytes): 0
	Major (requiring I/O) page faults: 22169
	Minor (reclaiming a frame) page faults: 80035959
	Voluntary context switches: 21730511
	Involuntary context switches: 4317241
	Swaps: 0
	File system inputs: 73144456
	File system outputs: 176920856
	Socket messages sent: 0
	Socket messages received: 0
	Signals delivered: 0
	Page size (bytes): 4096
	Exit status: 1
2026年 04月 06日 星期一 12:44:42 CST
(hiscanner_test) zxf@xglab2080ti:/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project$ 
(hiscanner_test) zxf@xglab2080ti:/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project$ 
(hiscanner_test) zxf@xglab2080ti:/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project$ cat config.yaml
# Required parameters - MUST BE SET
scan2_output: /stor/zxf/cnv/cnvguider/scan2/demo      # Path to SCAN2 results directory (e.g., "/path/to/scan2_out")
metadata_path: /stor/zxf/cnv/cnvguider/scan2/demo/metadata.tsv     # Path to metadata file (e.g., "./metadata.txt")
outdir: hiscanner_output_g1k_v37test           # Output directory for results (e.g., "./hiscanner_output")
use_multisample_segmentation: false  # Set to true to use multisample segmentation

# Reference data and external tools - MUST BE SET
fasta_folder: /stor/zxf/cnv/cnvguider/hiscanner_demo/human_g1k_v37_decoy_split          # Path to reference genome split by chromosome
mappability_folder_stem: /stor/zxf/cnv/cnvguider/hiscanner_demo/hg19CRG.100bp/hg19.CRC.100mer.  # Path to mappability files including the stem (e.g., "/path/to/hg19.CRC.100mer.")

# Analysis parameters - defaults provided but can be modified
rdr_only: false
binsize: 5000000 # 500000           # Bin size for analysis (in bp)
chrom_list: ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"]
lambda_range: [2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048]
lambda_value: 16          # edit this if you want to use a different lambda value for the final calls
max_wgd: 2               # Maximum whole genome duplication level
batch_size: 5            # Number of cells to process in parallel
depth_filter: 0          # Minimum read depth filter
ado_threshold: 0.2       # Allelic dropout threshold
threads: 4               # Number of parallel threads to use
ado_plot_baf_distribution: true  # Set to false to disable BAF distribution plots

# ADO analysis options
aggregate_every_k_snp: true  # Whether to aggregate every k SNPs for ADO analysis
k: 5                    # Number of SNPs to aggregate when aggregate_every_k_snp is true

# Debug and performance options
keep_raw_files: false    # Whether to keep intermediate raw files (default: false)
rerun: false            # Force rerun of existing results (default: false)
keep_temp_files: false  # Keep temporary files from multisample segmentation


# Cluster options
use_cluster: false      # Whether to use cluster for computation
cluster_queue: "park"   # Cluster queue to use
max_cluster_jobs: 100   # Maximum number of concurrent cluster jobs
(hiscanner_test) zxf@xglab2080ti:/stor/zxf/cnv/cnvguider/hiscanner_demo/my_project$ 

[yifnzhao]

Hi Xiaofei, it seems like the GMM step couldn't converge (unable to find an allelic balanced cluster to derived absolute copy number estimate), which might be due to high aneuploidy level or poor data quality. Can you confirm whether you are able to run the demo mouse data successfully? If so, the first diagnostic step I would recommend is to plot the read depth and BAF profile of this cell.