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Ploidy issue
See below
1.5.1 (Default)
-s workflow/Snakefile --config genecore=True genecore_prefix=/g/korbel/STOCKS/Data/Assay/sequencing/2024 genecore_date_folder=2024-07-24-HC7FTAFX7 genecore_regex_element=iTRU samples_to_process="[PC42PD6501]" plate_type=96 multistep_normalisation=True genome_browsing_files_generation=True MultiQC=True split_qc_plot=False publishdir=/g/korbel/WORKFLOW_RESULTS [email protected] data_location=/scratch/tweber/DATA/MC_DATA/STOCKS ashleys_pipeline_only=False ashleys_pipeline=True --nolock --rerun-incomplete --rerun-triggers mtime --conda-frontend mamba --profile /g/korbel2/weber/workspace/snakemake_workspace/snakemake_profiles/mosaicatcher-pipeline/v7/HPC/dev/slurm_legacy_conda
Conda only
HPC (slurm_legacy_conda)
MultiQC: true abs_path: / additional_sce_cutoff: 20000000 arbigent: false arbigent_bed_file: workflow/data/arbigent/manual_segmentation.bed arbigent_data: arbigent_mapability_track: workflow/data/arbigent/mapping_counts_allchrs_hg38.txt arbigent_mapability_track_h5: workflow/data/arbigent/mapping_counts_allchrs_hg38.h5 ashleys_pipeline: true ashleys_pipeline_only: false ashleys_pipeline_version: 2.3.4 ashleys_threshold: 0.5 blacklist_regions: true breakpointR: false breakpointR_only: false bypass_ashleys: false chromosomes: - chr1 - chr2 - chr3 - chr4 - chr5 - chr6 - chr7 - chr8 - chr9 - chr10 - chr11 - chr12 - chr13 - chr14 - chr15 - chr16 - chr17 - chr18 - chr19 - chr20 - chr21 - chr22 - chrX - chrY chromosomes_to_exclude: [] data_location: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7 email: [email protected] genecore: true genecore_date_folder: 2024-07-24-HC7FTAFX7 genecore_prefix: /g/korbel/STOCKS/Data/Assay/sequencing/2024 genecore_regex_element: iTRU genome_browsing_files_generation: true hand_selection: false hgsvc_based_normalized_counts: true input_bam_legacy: false list_commands: false methods: lenient: filter: 'FALSE' gtcutoff: 0 haplotags: true llr: 4 method_name: simpleCalls_llr4_poppriorsTRUE_haplotagsTRUE_gtcutoff0_regfactor6_filterFALSE poppriors: true regfactor: 6 stringent: filter: 'TRUE' gtcutoff: 0.05 haplotags: true llr: 4 method_name: simpleCalls_llr4_poppriorsTRUE_haplotagsFALSE_gtcutoff0.05_regfactor6_filterTRUE poppriors: true regfactor: 6 min_diff_jointseg: 0.1 min_diff_singleseg: 0.5 mosaicatcher_pipeline: true multistep_normalisation: true multistep_normalisation_for_SV_calling: false multistep_normalisation_options: min_reads_bin: 5 min_reads_cell: 100000 n_subsample: 1000 paired_end: true plate_type: 96 plottype_clustering: - position - chromosome plottype_consistency: - byaf - bypos plottype_counts: - raw - normalised publishdir: /g/korbel/WORKFLOW_RESULTS reference: hg38 references_data: T2T: R_reference: BSgenome.T2T.CHM13.V2 reference_fasta: workflow/data/ref_genomes/T2T.fa reference_file_location: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz segdups: workflow/data/segdups/segDups_T2T_UCSCtrack.bed.gz snv_sites_to_genotype: '' hg19: R_reference: BSgenome.Hsapiens.UCSC.hg19 reference_fasta: workflow/data/ref_genomes/hg19.fa reference_file_location: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/hg19.p13.plusMT.no_alt_analysis_set.fa.gz segdups: workflow/data/segdups/segDups_hg19_UCSCtrack.bed.gz snv_sites_to_genotype: '' hg38: R_reference: BSgenome.Hsapiens.UCSC.hg38 reference_fasta: workflow/data/ref_genomes/hg38.fa reference_file_location: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/hg38.analysisSet.fa.gz segdups: workflow/data/segdups/segDups_hg38_UCSCtrack.bed.gz snv_sites_to_genotype: '' mm10: R_reference: BSgenome.Mmusculus.UCSC.mm10 reference_fasta: workflow/data/ref_genomes/mm10.fa reference_file_location: https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.fa.gz segdups: workflow/data/segdups/segDups_mm10_UCSCtrack.bed.gz snv_sites_to_genotype: '' samples_to_process: - PC42PD6501 scNOVA: false scNOVA_scripts: annot_expressed: workflow/scripts/scNOVA_scripts/annot_expressed.R combine_features: workflow/scripts/scNOVA_scripts/combine_features.R count_norm: workflow/scripts/scNOVA_scripts/count_norm.R count_sort_annotate_chrid_CREs: workflow/scripts/scNOVA_scripts/count_sort_annotate_chrid_CREs.R count_sort_annotate_geneid: workflow/scripts/scNOVA_scripts/count_sort_annotate_geneid.R count_sort_label: workflow/scripts/scNOVA_scripts/count_sort_label.R feature_sc_var: workflow/scripts/scNOVA_scripts/feature_sc_var.R generate_CN_for_CNN: workflow/scripts/scNOVA_scripts/generate_CN_for_CNN.R generate_CN_for_chromVAR: workflow/scripts/scNOVA_scripts/generate_CN_for_chromVAR.R infer_diff_gene_expression: workflow/scripts/scNOVA_scripts/infer_diff_gene_expression.R infer_diff_gene_expression_alt: workflow/scripts/scNOVA_scripts/infer_diff_gene_expression_alt.R scTRIP_multiplot: false sce_min_distance: 500000 split_qc_plot: false strandscape_labels_path: '' use_light_data: false version: 2.3.4 whatshap_only: false window: 200000
│ File: errors/estimate_ploidy/7509162.error ───────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 1 │ Config file config/config.yaml is extended by additional config specified via the command line. 2 │ localrules directive specifies rules that are not present in the Snakefile: 3 │ symlink_bam_ashleys 4 │ ashleys_symlink_selected_bam 5 │ 6 │ Building DAG of jobs... 7 │ Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (f │ or details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config │ --set channel_priority strict'. 8 │ Using shell: /usr/bin/bash 9 │ Provided cores: 48 10 │ Rules claiming more threads will be scaled down. 11 │ Provided resources: mem_mb=64000, mem_mib=61036, disk_mb=1000, disk_mib=954 12 │ Singularity containers: ignored 13 │ Select jobs to execute... 14 │ 15 │ [Fri Jul 26 10:49:12 2024] 16 │ rule estimate_ploidy: 17 │ input: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/counts/PC42PD6501.txt.sort.gz 18 │ output: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/ploidy/ploidy_detailled.txt 19 │ log: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/log/estimate_ploidy/PC42PD6501.log 20 │ jobid: 0 21 │ reason: Missing output files: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/ploidy/ploidy_detailled.txt 22 │ wildcards: folder=/scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7, sample=PC42PD6501 23 │ threads: 48 24 │ resources: mem_mb=64000, mem_mib=61036, disk_mb=1000, disk_mib=954, tmpdir=/scratch/jobs/7509162, partition=htc, qos=normal, time=01:00:00, c │ onstraint= 25 │ 26 │ Activating conda environment: .snakemake/conda/00463f690660aba39f8cad571dd5b22d_ 27 │ /g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/.snakemake/conda/00463f690660aba39f8cad571dd5b22d_/li │ b/python3.12/site-packages/scipy/stats/_distn_infrastructure.py:2027: RuntimeWarning: divide by zero encountered in divide 28 │ x = np.asarray((x - loc)/scale, dtype=dtyp) 29 │ /g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/.snakemake/conda/00463f690660aba39f8cad571dd5b22d_/li │ b/python3.12/site-packages/scipy/stats/_distn_infrastructure.py:2027: RuntimeWarning: invalid value encountered in divide 30 │ x = np.asarray((x - loc)/scale, dtype=dtyp) 31 │ multiprocessing.pool.RemoteTraceback: 32 │ """ 33 │ Traceback (most recent call last): 34 │ File "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/.snakemake/conda/00463f690660aba39f8cad571dd5 │ b22d_/lib/python3.12/multiprocessing/pool.py", line 125, in worker 35 │ result = (True, func(*args, **kwds)) 36 │ ^^^^^^^^^^^^^^^^^^^ 37 │ File "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/workflow/scripts/ploidy/ploidy_estimator.py", │ line 557, in process_segment 38 │ mixture.fit_stddevs_meanprop(frac_values) 39 │ File "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/workflow/scripts/ploidy/ploidy_estimator.py", │ line 153, in fit_stddevs_meanprop 40 │ assert not np.isnan(new_v), "new_v is NaN in iteration: {}".format(n) 41 │ ^^^^^^^^^^^^^^^^^^^ 42 │ AssertionError: ('new_v is NaN in iteration: 5', 'segment_id', 'chr21', 7000000, 8000000) 43 │ """ 44 │ 45 │ The above exception was the direct cause of the following exception: 46 │ 47 │ Traceback (most recent call last): 48 │ File "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/workflow/scripts/ploidy/ploidy_estimator.py", │ line 635, in <module> 49 │ main() 50 │ File "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/workflow/scripts/ploidy/ploidy_estimator.py", │ line 624, in main 51 │ ploidy_estimates = run_ploidy_estimation(frac_dataset, args.max_ploidy, args.alpha, args.background, args.jobs) 52 │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 53 │ File "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/workflow/scripts/ploidy/ploidy_estimator.py", │ line 495, in run_ploidy_estimation 54 │ for row in resiter: 55 │ File "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/.snakemake/conda/00463f690660aba39f8cad571dd5 │ b22d_/lib/python3.12/multiprocessing/pool.py", line 873, in next 56 │ raise value 57 │ AssertionError: ('new_v is NaN in iteration: 5', 'segment_id', 'chr21', 7000000, 8000000) 58 │ [Fri Jul 26 10:49:14 2024] 59 │ Error in rule estimate_ploidy: 60 │ jobid: 0 61 │ input: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/counts/PC42PD6501.txt.sort.gz 62 │ output: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/ploidy/ploidy_detailled.txt 63 │ log: /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/log/estimate_ploidy/PC42PD6501.log (check log file(s) for error details) 64 │ conda-env: /g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/.snakemake/conda/00463f690660aba39f8ca │ d571dd5b22d_ 65 │ shell: 66 │ 67 │ python workflow/scripts/ploidy/ploidy_estimator.py --debug --merge-bins-to 1000000 --shift-window-by 1000000 │ --max-ploidy 6 --boundary-alpha 0.05 --jobs 48 --input /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24 │ -HC7FTAFX7/PC42PD6501/counts/PC42PD6501.txt.sort.gz --output /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/ploi │ dy/ploidy_detailled.txt --log /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/log/estimate_ploidy/PC42PD6501.log 68 │ 69 │ (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) 70 │ 71 │ Shutting down, this might take some time. 72 │ Exiting because a job execution failed. Look above for error message
### Anything else? Data:
zcat /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/counts/PC42PD6501.txt.sort.gz | grep chr21 | less chr21 0 200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 200000 400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 400000 600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 600000 800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 800000 1000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 1000000 1200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 1200000 1400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 1400000 1600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 1600000 1800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 1800000 2000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 2000000 2200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 2200000 2400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 2400000 2600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 2600000 2800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 2800000 3000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 3000000 3200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 3200000 3400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 3400000 3600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 3600000 3800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 3800000 4000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 4000000 4200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 4200000 4400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 4400000 4600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 4600000 4800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 4800000 5000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 5000000 5200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 5200000 5400000 PC42PD6501 PC42PD6501iTRU7G84 5.65150881429789 8.47726322144683 WC chr21 5400000 5600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 5600000 5800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 5800000 6000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 6000000 6200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 6200000 6400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 6400000 6600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 6600000 6800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 6800000 7000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 7000000 7200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 7200000 7400000 PC42PD6501 PC42PD6501iTRU7G84 7.04378733968665 7.04378733968665 WC chr21 7400000 7600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 7600000 7800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 7800000 8000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 8000000 8200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 8200000 8400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 8400000 8600000 PC42PD6501 PC42PD6501iTRU7G84 1.42862819333112 2.85725638666224 WC chr21 8600000 8800000 PC42PD6501 PC42PD6501iTRU7G84 12.8819929511762 5.72533020052276 WC chr21 8800000 9000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 9000000 9200000 PC42PD6501 PC42PD6501iTRU7G84 3.62154424211843 6.33770242370726 WC chr21 9200000 9400000 PC42PD6501 PC42PD6501iTRU7G84 5.48200634763216 9.59351110835628 WC chr21 9400000 9600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 9600000 9800000 PC42PD6501 PC42PD6501iTRU7G84 5.64505750202717 4.23379312652038 WC chr21 9800000 10000000 PC42PD6501 PC42PD6501iTRU7G84 7.27567429502113 17.8584732695973 WC chr21 10000000 10200000 PC42PD6501 PC42PD6501iTRU7G84 8.6572091912337 1.44286819853895 WC chr21 10200000 10400000 PC42PD6501 PC42PD6501iTRU7G84 7.01716821993424 7.01716821993424 WC chr21 10400000 10600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 10600000 10800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 10800000 11000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 11000000 11200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 11200000 11400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 11400000 11600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 11600000 11800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 11800000 12000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 12000000 12200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 12200000 12400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 12400000 12600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 12600000 12800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 12800000 13000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 13000000 13200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 13200000 13400000 PC42PD6501 PC42PD6501iTRU7G84 3.62834903782206 9.67559743419216 WC chr21 13400000 13600000 PC42PD6501 PC42PD6501iTRU7G84 10.536002747909 7.90200206093178 WC chr21 13600000 13800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 13800000 14000000 PC42PD6501 PC42PD6501iTRU7G84 5.71835162343952 15.2489376625054 WC chr21 14000000 14200000 PC42PD6501 PC42PD6501iTRU7G84 6.01886236123176 19.0597308105672 WC chr21 14200000 14400000 PC42PD6501 PC42PD6501iTRU7G84 8.11692655972695 17.3934140565577 WC chr21 14400000 14600000 PC42PD6501 PC42PD6501iTRU7G84 8.47122513703207 12.1017501957601 WC chr21 14600000 14800000 PC42PD6501 PC42PD6501iTRU7G84 3.46088136203631 24.2261695342542 WC chr21 14800000 15000000 PC42PD6501 PC42PD6501iTRU7G84 16.8026218764187 23.5236706269862 WC chr21 15000000 15200000 PC42PD6501 PC42PD6501iTRU7G84 6.57965038337274 16.4491259584318 WC chr21 15200000 15400000 PC42PD6501 PC42PD6501iTRU7G84 9.48219738008985 16.8572397868264 WC chr21 15400000 15600000 PC42PD6501 PC42PD6501iTRU7G84 8.27502305920632 21.7219355304166 WC chr21 15600000 15800000 PC42PD6501 PC42PD6501iTRU7G84 10.6221718212467 14.1628957616623 WC chr21 15800000 16000000 PC42PD6501 PC42PD6501iTRU7G84 7.38452273872794 11.0767841080919 WC chr21 16000000 16200000 PC42PD6501 PC42PD6501iTRU7G84 7.46607444588726 16.1764946327557 WC chr21 16200000 16400000 PC42PD6501 PC42PD6501iTRU7G84 4.95243464804436 21.0478472541885 WC chr21 16400000 16600000 PC42PD6501 PC42PD6501iTRU7G84 9.36909190082159 12.0459753010563 WC chr21 16600000 16800000 PC42PD6501 PC42PD6501iTRU7G84 9.59062805591344 21.5789131258052 WC chr21 16800000 17000000 PC42PD6501 PC42PD6501iTRU7G84 8.27549739107602 17.7332086951629 WC chr21 17000000 17200000 PC42PD6501 PC42PD6501iTRU7G84 10.844560003049 15.1823840042686 WC chr21 17200000 17400000 PC42PD6501 PC42PD6501iTRU7G84 11.6999488354899 15.9544756847589 WC chr21 17400000 17600000 PC42PD6501 PC42PD6501iTRU7G84 20.2922204487124 11.2734558048402 WC chr21 17600000 17800000 PC42PD6501 PC42PD6501iTRU7G84 6.39470883171324 20.2499113004253 WC chr21 17800000 18000000 PC42PD6501 PC42PD6501iTRU7G84 6.5404230369261 9.81063455538915 WC chr21 18000000 18200000 PC42PD6501 PC42PD6501iTRU7G84 11.1855078713237 14.5411602327208 WC chr21 18200000 18400000 PC42PD6501 PC42PD6501iTRU7G84 11.2174429550385 16.2029731572778 WC chr21 18400000 18600000 PC42PD6501 PC42PD6501iTRU7G84 13.5552726310354 20.9490577025093 WC chr21 18600000 18800000 PC42PD6501 PC42PD6501iTRU7G84 3.65933453349687 13.4175599561552 WC chr21 18800000 19000000 PC42PD6501 PC42PD6501iTRU7G84 8.52883246632305 8.52883246632305 WC chr21 19000000 19200000 PC42PD6501 PC42PD6501iTRU7G84 8.55824772173749 14.6712818086928 WC chr21 19200000 19400000 PC42PD6501 PC42PD6501iTRU7G84 8.08332290509794 13.4722048418299 WC chr21 19400000 19600000 PC42PD6501 PC42PD6501iTRU7G84 4.86112478276688 12.1528119569172 WC chr21 19600000 19800000 PC42PD6501 PC42PD6501iTRU7G84 12.7028787873581 16.5137424235655 WC chr21 19800000 20000000 PC42PD6501 PC42PD6501iTRU7G84 11.5313013373021 11.5313013373021 WC chr21 20000000 20200000 PC42PD6501 PC42PD6501iTRU7G84 4.93511779764684 13.5715739435288 WC chr21 20200000 20400000 PC42PD6501 PC42PD6501iTRU7G84 8.0148173207781 13.3580288679635 WC chr21 20400000 20600000 PC42PD6501 PC42PD6501iTRU7G84 7.29835739310348 18.2458934827587 WC chr21 20600000 20800000 PC42PD6501 PC42PD6501iTRU7G84 10.8232863521421 24.0517474492046 WC chr21 20800000 21000000 PC42PD6501 PC42PD6501iTRU7G84 6.23461787644935 19.9507772046379 WC chr21 21000000 21200000 PC42PD6501 PC42PD6501iTRU7G84 11.9428323017189 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9.74707006004525 WC chr21 41200000 41400000 PC42PD6501 PC42PD6501iTRU7G84 7.27172023192581 14.5434404638516 WC chr21 41400000 41600000 PC42PD6501 PC42PD6501iTRU7G84 3.27925558471771 18.0359057159474 WC chr21 41600000 41800000 PC42PD6501 PC42PD6501iTRU7G84 6.64134010146379 11.0689001691063 WC chr21 41800000 42000000 PC42PD6501 PC42PD6501iTRU7G84 5.77846712994918 9.08044834706299 WC chr21 42000000 42200000 PC42PD6501 PC42PD6501iTRU7G84 8.0639622090602 18.3271868387732 WC chr21 42200000 42400000 PC42PD6501 PC42PD6501iTRU7G84 6.53785840008038 10.1700019556806 WC chr21 42400000 42600000 PC42PD6501 PC42PD6501iTRU7G84 9.20820938422024 16.8817172044038 WC chr21 42600000 42800000 PC42PD6501 PC42PD6501iTRU7G84 9.085407216229 14.3852280923626 WC chr21 42800000 43000000 PC42PD6501 PC42PD6501iTRU7G84 8.00430073911341 16.0086014782268 WC chr21 43000000 43200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 43200000 43400000 PC42PD6501 PC42PD6501iTRU7G84 2.60028551678039 11.2679039060483 WC chr21 43400000 43600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 43600000 43800000 PC42PD6501 PC42PD6501iTRU7G84 7.78811147816119 12.9801857969353 WC chr21 43800000 44000000 PC42PD6501 PC42PD6501iTRU7G84 6.55191620250049 19.6557486075015 WC chr21 44000000 44200000 PC42PD6501 PC42PD6501iTRU7G84 9.006551540609 6.433251100435 WC chr21 44200000 44400000 PC42PD6501 PC42PD6501iTRU7G84 4.43647206380232 7.98564971484418 WC chr21 44400000 44600000 PC42PD6501 PC42PD6501iTRU7G84 6.49726074302116 12.9945214860423 WC chr21 44600000 44800000 PC42PD6501 PC42PD6501iTRU7G84 5.5912481734828 9.58499686882766 WC chr21 44800000 45000000 PC42PD6501 PC42PD6501iTRU7G84 7.45738748524617 12.6775587249185 WC chr21 45000000 45200000 PC42PD6501 PC42PD6501iTRU7G84 8.3383054998096 16.6766109996192 WC chr21 45200000 45400000 PC42PD6501 PC42PD6501iTRU7G84 8.22797691896552 12.7159643293103 WC chr21 45400000 45600000 PC42PD6501 PC42PD6501iTRU7G84 4.19102768904602 7.68355076325104 WC chr21 45600000 45800000 PC42PD6501 PC42PD6501iTRU7G84 8.11218991907554 14.4216709672454 WC chr21 45800000 46000000 PC42PD6501 PC42PD6501iTRU7G84 2.8265000843503 7.77287523196331 WC chr21 46000000 46200000 PC42PD6501 PC42PD6501iTRU7G84 5.21280408784654 10.4256081756931 WC chr21 46200000 46400000 PC42PD6501 PC42PD6501iTRU7G84 6.86310933598208 11.1525526709709 WC chr21 46400000 46600000 PC42PD6501 PC42PD6501iTRU7G84 9.40875826524655 16.9357648774438 WC chr21 46600000 46709983 PC42PD6501 PC42PD6501iTRU7G84 9.98362480227455 7.13116057305325 WC (END) [ seneca ][ (0*$bash) ][MC_FIX][ 07-26 14:21 ] chr21 37200000 37400000 PC42PD6501 PC42PD6501iTRU7G84 11.6294793746355 12.6867047723297 WC chr21 37400000 37600000 PC42PD6501 PC42PD6501iTRU7G84 14.4377065535592 17.5315008150362 WC chr21 37600000 37800000 PC42PD6501 PC42PD6501iTRU7G84 6.29472686166693 18.8841805850008 WC chr21 37800000 38000000 PC42PD6501 PC42PD6501iTRU7G84 11.7928944743716 19.3740409221819 WC chr21 38000000 38200000 PC42PD6501 PC42PD6501iTRU7G84 8.15752991232099 22.6598053120027 WC chr21 38200000 38400000 PC42PD6501 PC42PD6501iTRU7G84 3.37055650990527 16.8527825495264 WC chr21 38400000 38600000 PC42PD6501 PC42PD6501iTRU7G84 8.07990388165859 21.5464103510896 WC chr21 38600000 38800000 PC42PD6501 PC42PD6501iTRU7G84 10.7821501806552 19.7672753312011 WC chr21 38800000 39000000 PC42PD6501 PC42PD6501iTRU7G84 6.45022399433312 12.9004479886662 WC chr21 39000000 39200000 PC42PD6501 PC42PD6501iTRU7G84 6.5803083371218 13.9831552163838 WC chr21 39200000 39400000 PC42PD6501 PC42PD6501iTRU7G84 3.6297184358856 24.198122905904 WC chr21 39400000 39600000 PC42PD6501 PC42PD6501iTRU7G84 9.7207330119831 17.4973194215696 WC chr21 39600000 39800000 PC42PD6501 PC42PD6501iTRU7G84 13.084079194294 22.0793836403711 WC chr21 39800000 40000000 PC42PD6501 PC42PD6501iTRU7G84 8.81648341754569 10.419480402554 WC chr21 40000000 40200000 PC42PD6501 PC42PD6501iTRU7G84 7.65469705789747 13.6083503251511 WC chr21 40200000 40400000 PC42PD6501 PC42PD6501iTRU7G84 8.69145143320243 14.4857523886707 WC chr21 40400000 40600000 PC42PD6501 PC42PD6501iTRU7G84 5.0814070921012 12.1953770210429 WC chr21 40600000 40800000 PC42PD6501 PC42PD6501iTRU7G84 6.68680371962728 16.239380461952 WC chr21 40800000 41000000 PC42PD6501 PC42PD6501iTRU7G84 11.6020933060086 12.4945620218554 WC chr21 41000000 41200000 PC42PD6501 PC42PD6501iTRU7G84 7.31030254503394 9.74707006004525 WC chr21 41200000 41400000 PC42PD6501 PC42PD6501iTRU7G84 7.27172023192581 14.5434404638516 WC chr21 41400000 41600000 PC42PD6501 PC42PD6501iTRU7G84 3.27925558471771 18.0359057159474 WC chr21 41600000 41800000 PC42PD6501 PC42PD6501iTRU7G84 6.64134010146379 11.0689001691063 WC chr21 41800000 42000000 PC42PD6501 PC42PD6501iTRU7G84 5.77846712994918 9.08044834706299 WC chr21 42000000 42200000 PC42PD6501 PC42PD6501iTRU7G84 8.0639622090602 18.3271868387732 WC chr21 42200000 42400000 PC42PD6501 PC42PD6501iTRU7G84 6.53785840008038 10.1700019556806 WC chr21 42400000 42600000 PC42PD6501 PC42PD6501iTRU7G84 9.20820938422024 16.8817172044038 WC chr21 42600000 42800000 PC42PD6501 PC42PD6501iTRU7G84 9.085407216229 14.3852280923626 WC chr21 42800000 43000000 PC42PD6501 PC42PD6501iTRU7G84 8.00430073911341 16.0086014782268 WC chr21 43000000 43200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 43200000 43400000 PC42PD6501 PC42PD6501iTRU7G84 2.60028551678039 11.2679039060483 WC chr21 43400000 43600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0 chr21 43600000 43800000 PC42PD6501 PC42PD6501iTRU7G84 7.78811147816119 12.9801857969353 WC chr21 43800000 44000000 PC42PD6501 PC42PD6501iTRU7G84 6.55191620250049 19.6557486075015 WC chr21 44000000 44200000 PC42PD6501 PC42PD6501iTRU7G84 9.006551540609 6.433251100435 WC chr21 44200000 44400000 PC42PD6501 PC42PD6501iTRU7G84 4.43647206380232 7.98564971484418 WC chr21 44400000 44600000 PC42PD6501 PC42PD6501iTRU7G84 6.49726074302116 12.9945214860423 WC chr21 44600000 44800000 PC42PD6501 PC42PD6501iTRU7G84 5.5912481734828 9.58499686882766 WC chr21 44800000 45000000 PC42PD6501 PC42PD6501iTRU7G84 7.45738748524617 12.6775587249185 WC chr21 45000000 45200000 PC42PD6501 PC42PD6501iTRU7G84 8.3383054998096 16.6766109996192 WC chr21 45200000 45400000 PC42PD6501 PC42PD6501iTRU7G84 8.22797691896552 12.7159643293103 WC chr21 45400000 45600000 PC42PD6501 PC42PD6501iTRU7G84 4.19102768904602 7.68355076325104 WC chr21 45600000 45800000 PC42PD6501 PC42PD6501iTRU7G84 8.11218991907554 14.4216709672454 WC chr21 45800000 46000000 PC42PD6501 PC42PD6501iTRU7G84 2.8265000843503 7.77287523196331 WC chr21 46000000 46200000 PC42PD6501 PC42PD6501iTRU7G84 5.21280408784654 10.4256081756931 WC chr21 46200000 46400000 PC42PD6501 PC42PD6501iTRU7G84 6.86310933598208 11.1525526709709 WC chr21 46400000 46600000 PC42PD6501 PC42PD6501iTRU7G84 9.40875826524655 16.9357648774438 WC chr21 46600000 46709983 PC42PD6501 PC42PD6501iTRU7G84 9.98362480227455 7.13116057305325 WC
The text was updated successfully, but these errors were encountered:
weber8thomas
No branches or pull requests
Contact Details
[email protected]
What happened?
Ploidy issue
Steps To Reproduce
See below
Mosaicatcher-pipeline Version
1.5.1 (Default)
Command used
How did you run the pipeline?
Conda only
What did you use to run the pipeline? (local execution, HPC, cloud)
HPC (slurm_legacy_conda)
Pipeline configuration file
Relevant log output
zcat /scratch/tweber/DATA/MC_DATA/STOCKS/2024-07-24-HC7FTAFX7/PC42PD6501/counts/PC42PD6501.txt.sort.gz | grep chr21 | less
chr21 0 200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 200000 400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 400000 600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 600000 800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 800000 1000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 1000000 1200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 1200000 1400000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 1400000 1600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 1600000 1800000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 1800000 2000000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
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chr21 44400000 44600000 PC42PD6501 PC42PD6501iTRU7G84 6.49726074302116 12.9945214860423 WC
chr21 44600000 44800000 PC42PD6501 PC42PD6501iTRU7G84 5.5912481734828 9.58499686882766 WC
chr21 44800000 45000000 PC42PD6501 PC42PD6501iTRU7G84 7.45738748524617 12.6775587249185 WC
chr21 45000000 45200000 PC42PD6501 PC42PD6501iTRU7G84 8.3383054998096 16.6766109996192 WC
chr21 45200000 45400000 PC42PD6501 PC42PD6501iTRU7G84 8.22797691896552 12.7159643293103 WC
chr21 45400000 45600000 PC42PD6501 PC42PD6501iTRU7G84 4.19102768904602 7.68355076325104 WC
chr21 45600000 45800000 PC42PD6501 PC42PD6501iTRU7G84 8.11218991907554 14.4216709672454 WC
chr21 45800000 46000000 PC42PD6501 PC42PD6501iTRU7G84 2.8265000843503 7.77287523196331 WC
chr21 46000000 46200000 PC42PD6501 PC42PD6501iTRU7G84 5.21280408784654 10.4256081756931 WC
chr21 46200000 46400000 PC42PD6501 PC42PD6501iTRU7G84 6.86310933598208 11.1525526709709 WC
chr21 46400000 46600000 PC42PD6501 PC42PD6501iTRU7G84 9.40875826524655 16.9357648774438 WC
chr21 46600000 46709983 PC42PD6501 PC42PD6501iTRU7G84 9.98362480227455 7.13116057305325 WC
(END)
[ seneca ][ (0*$bash) ][MC_FIX][ 07-26 14:21 ]
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chr21 37400000 37600000 PC42PD6501 PC42PD6501iTRU7G84 14.4377065535592 17.5315008150362 WC
chr21 37600000 37800000 PC42PD6501 PC42PD6501iTRU7G84 6.29472686166693 18.8841805850008 WC
chr21 37800000 38000000 PC42PD6501 PC42PD6501iTRU7G84 11.7928944743716 19.3740409221819 WC
chr21 38000000 38200000 PC42PD6501 PC42PD6501iTRU7G84 8.15752991232099 22.6598053120027 WC
chr21 38200000 38400000 PC42PD6501 PC42PD6501iTRU7G84 3.37055650990527 16.8527825495264 WC
chr21 38400000 38600000 PC42PD6501 PC42PD6501iTRU7G84 8.07990388165859 21.5464103510896 WC
chr21 38600000 38800000 PC42PD6501 PC42PD6501iTRU7G84 10.7821501806552 19.7672753312011 WC
chr21 38800000 39000000 PC42PD6501 PC42PD6501iTRU7G84 6.45022399433312 12.9004479886662 WC
chr21 39000000 39200000 PC42PD6501 PC42PD6501iTRU7G84 6.5803083371218 13.9831552163838 WC
chr21 39200000 39400000 PC42PD6501 PC42PD6501iTRU7G84 3.6297184358856 24.198122905904 WC
chr21 39400000 39600000 PC42PD6501 PC42PD6501iTRU7G84 9.7207330119831 17.4973194215696 WC
chr21 39600000 39800000 PC42PD6501 PC42PD6501iTRU7G84 13.084079194294 22.0793836403711 WC
chr21 39800000 40000000 PC42PD6501 PC42PD6501iTRU7G84 8.81648341754569 10.419480402554 WC
chr21 40000000 40200000 PC42PD6501 PC42PD6501iTRU7G84 7.65469705789747 13.6083503251511 WC
chr21 40200000 40400000 PC42PD6501 PC42PD6501iTRU7G84 8.69145143320243 14.4857523886707 WC
chr21 40400000 40600000 PC42PD6501 PC42PD6501iTRU7G84 5.0814070921012 12.1953770210429 WC
chr21 40600000 40800000 PC42PD6501 PC42PD6501iTRU7G84 6.68680371962728 16.239380461952 WC
chr21 40800000 41000000 PC42PD6501 PC42PD6501iTRU7G84 11.6020933060086 12.4945620218554 WC
chr21 41000000 41200000 PC42PD6501 PC42PD6501iTRU7G84 7.31030254503394 9.74707006004525 WC
chr21 41200000 41400000 PC42PD6501 PC42PD6501iTRU7G84 7.27172023192581 14.5434404638516 WC
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chr21 41600000 41800000 PC42PD6501 PC42PD6501iTRU7G84 6.64134010146379 11.0689001691063 WC
chr21 41800000 42000000 PC42PD6501 PC42PD6501iTRU7G84 5.77846712994918 9.08044834706299 WC
chr21 42000000 42200000 PC42PD6501 PC42PD6501iTRU7G84 8.0639622090602 18.3271868387732 WC
chr21 42200000 42400000 PC42PD6501 PC42PD6501iTRU7G84 6.53785840008038 10.1700019556806 WC
chr21 42400000 42600000 PC42PD6501 PC42PD6501iTRU7G84 9.20820938422024 16.8817172044038 WC
chr21 42600000 42800000 PC42PD6501 PC42PD6501iTRU7G84 9.085407216229 14.3852280923626 WC
chr21 42800000 43000000 PC42PD6501 PC42PD6501iTRU7G84 8.00430073911341 16.0086014782268 WC
chr21 43000000 43200000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
chr21 43200000 43400000 PC42PD6501 PC42PD6501iTRU7G84 2.60028551678039 11.2679039060483 WC
chr21 43400000 43600000 PC42PD6501 PC42PD6501iTRU7G84 0.0 0.0
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chr21 43800000 44000000 PC42PD6501 PC42PD6501iTRU7G84 6.55191620250049 19.6557486075015 WC
chr21 44000000 44200000 PC42PD6501 PC42PD6501iTRU7G84 9.006551540609 6.433251100435 WC
chr21 44200000 44400000 PC42PD6501 PC42PD6501iTRU7G84 4.43647206380232 7.98564971484418 WC
chr21 44400000 44600000 PC42PD6501 PC42PD6501iTRU7G84 6.49726074302116 12.9945214860423 WC
chr21 44600000 44800000 PC42PD6501 PC42PD6501iTRU7G84 5.5912481734828 9.58499686882766 WC
chr21 44800000 45000000 PC42PD6501 PC42PD6501iTRU7G84 7.45738748524617 12.6775587249185 WC
chr21 45000000 45200000 PC42PD6501 PC42PD6501iTRU7G84 8.3383054998096 16.6766109996192 WC
chr21 45200000 45400000 PC42PD6501 PC42PD6501iTRU7G84 8.22797691896552 12.7159643293103 WC
chr21 45400000 45600000 PC42PD6501 PC42PD6501iTRU7G84 4.19102768904602 7.68355076325104 WC
chr21 45600000 45800000 PC42PD6501 PC42PD6501iTRU7G84 8.11218991907554 14.4216709672454 WC
chr21 45800000 46000000 PC42PD6501 PC42PD6501iTRU7G84 2.8265000843503 7.77287523196331 WC
chr21 46000000 46200000 PC42PD6501 PC42PD6501iTRU7G84 5.21280408784654 10.4256081756931 WC
chr21 46200000 46400000 PC42PD6501 PC42PD6501iTRU7G84 6.86310933598208 11.1525526709709 WC
chr21 46400000 46600000 PC42PD6501 PC42PD6501iTRU7G84 9.40875826524655 16.9357648774438 WC
chr21 46600000 46709983 PC42PD6501 PC42PD6501iTRU7G84 9.98362480227455 7.13116057305325 WC
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