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Published 20 hours ago • verified publisher icon singleron-RD

snp target_metrics FileNotFoundError(f'No file found for {pattern_list}')

Open PhilippBanza opened this issue 1 year ago • 1 comments

Hi, I need help with the snp assay:

Describe the bug During the snp run I receive an FileNotFoundError at step target_metrics:

2023-09-01 23:17:01,724 - celescope.tools.barcode.add_step_metrics - INFO - done. time used: 0:00:00.000327 2023-09-01 23:17:01,727 - celescope.tools.barcode.run - INFO - done. time used: 9:03:02.122252 2023-09-01 23:17:01,727 - celescope.tools.step._clean_up - INFO - start... 2023-09-01 23:17:01,744 - celescope.tools.step._render_html - INFO - start... 2023-09-01 23:17:02,506 - celescope.tools.step._render_html - INFO - done. time used: 0:00:00.761477 2023-09-01 23:17:02,506 - celescope.tools.step._clean_up - INFO - done. time used: 0:00:00.779391 2023-09-01 23:17:02,506 - celescope.tools.barcode.barcode - INFO - done. time used: 9:03:03.698185 2023-09-01 23:35:32,885 - celescope.tools.step._clean_up - INFO - start... 2023-09-01 23:35:32,907 - celescope.tools.step._render_html - INFO - start... 2023-09-01 23:35:33,505 - celescope.tools.step._render_html - INFO - done. time used: 0:00:00.597490 2023-09-01 23:35:33,505 - celescope.tools.step._clean_up - INFO - done. time used: 0:00:00.620049 2023-09-01 23:35:33,511 - celescope.tools.featureCounts.featureCounts - INFO - done. time used: 3:43:20.455596 2023-09-01 23:35:41,546 - celescope.tools.target_metrics.target_metrics - INFO - start... CeleScope version: 1.17.0 Args: Namespace(subparser_assay='snp', gene_list=None, panel='lung_1', bam='.//KM1_RNA_test/05.featureCounts/KM1_RNA_test_aligned_posSorted_addTag.bam', match_dir='./result_celesco_RNA_test', thread='20', debug=False, func=<function target_metrics at 0x7fb70e3ab040>) 2023-09-01 23:35:41,597 - celescope.tools.utils.get_barcode_from_match_dir - INFO - start... 2023-09-01 23:35:41,597 - celescope.tools.utils.get_matrix_dir_from_match_dir - INFO - start... Traceback (most recent call last): File "/home/philipp_bs/miniconda3/envs/celescope/bin/celescope", line 8, in sys.exit(main()) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main args.func(args) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper result = func(*args, **kwargs) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/target_metrics.py", line 163, in target_metrics with Target_metrics(args, display_title='Target Enrichment') as runner: File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/target_metrics.py", line 42, in init self.match_barcode_list, self.n_cell = utils.get_barcode_from_match_dir(args.match_dir) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper result = func(*args, **kwargs) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 306, in get_barcode_from_match_dir matrix_dir = get_matrix_dir_from_match_dir(match_dir) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper result = func(*args, **kwargs) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 292, in get_matrix_dir_from_match_dir matrix_dir = glob_file(matrix_dir_pattern_list) File "/home/philipp_bs/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 247, in glob_file raise FileNotFoundError(f'No file found for {pattern_list}') FileNotFoundError: No file found for ['./result_celescope_KM1_total/*count/*filtered_feature_bc_matrix', './result_celescope_KM1_total/*count/*matrix_10X'] 2023-09-01 23:35:44,461 - celescope.snp.variant_calling.variant_calling - INFO - start...

Shell script:

celescope snp sample --outdir .//KM1_RNA_test/00.sample --sample KM1_RNA_test --thread 20 --chemistry auto  --fq1 ./lane_1/fast_dir/KM1_S138788_1_R1.fastq,./lane_2/fast_dir/KM1_S138788_2_R1.fastq,./lane_1/KM1_enriched_S138790_1_R1.fastq,./lane_2/KM1_enriched_S138790_2_R1.fastq 
celescope snp barcode --outdir .//KM1_RNA_test/01.barcode --sample KM1_RNA_test --thread 20 --chemistry auto --lowNum 2  --fq1 ./lane_1/fast_dir/KM1_S138788_1_R1.fastq,./lane_2/fast_dir/KM1_S138788_2_R1.fastq,./lane_1/KM1_enriched_S138790_1_R1.fastq,./lane_2/KM1_enriched_S138790_2_R1.fastq --fq2 ./lane_1/fast_dir/KM1_S138788_1_R2.fastq,./lane_2/fast_dir/KM1_S138788_2_R2.fastq,./lane_1/KM1_enriched_S138790_1_R2.fastq,./lane_2/KM1_enriched_S138790_2_R2.fastq 
celescope snp cutadapt --outdir .//KM1_RNA_test/02.cutadapt --sample KM1_RNA_test --thread 20 --minimum_length 20 --nextseq_trim 20 --overlap 10  --fq .//KM1_RNA_test/01.barcode/KM1_RNA_test_2.fq 
celescope snp consensus --outdir .//KM1_RNA_test/03.consensus --sample KM1_RNA_test --thread 20 --threshold 0.5 --not_consensus --min_consensus_read 1  --fq .//KM1_RNA_test/02.cutadapt/KM1_RNA_test_clean_2.fq 
celescope snp star --outdir .//KM1_RNA_test/04.star --sample KM1_RNA_test --thread 20 --genomeDir /home/philipp_bs/bioinf_isilon/Research/HUTTER/Internal/philipp_bioinf/singleron/hs_ensembl_110 --outFilterMatchNmin 50 --outFilterMultimapNmax 1 --starMem 30  --fq .//KM1_RNA_test/02.cutadapt/KM1_RNA_test_clean_2.fq 
celescope snp featureCounts --outdir .//KM1_RNA_test/05.featureCounts --sample KM1_RNA_test --thread 20 --gtf_type gene --genomeDir /home/philipp_bs/bioinf_isilon/Research/HUTTER/Internal/philipp_bioinf/singleron/hs_ensembl_110  --input .//KM1_RNA_test/04.star/KM1_RNA_test_Aligned.out.bam 
celescope snp target_metrics --outdir .//KM1_RNA_test/06.target_metrics --sample KM1_RNA_test --thread 20 --panel lung_1  --bam .//KM1_RNA_test/05.featureCounts/KM1_RNA_test_aligned_posSorted_addTag.bam --match_dir ./result_celescope_KM1_total --add_RG 
celescope snp variant_calling --outdir .//KM1_RNA_test/07.variant_calling --sample KM1_RNA_test --thread 20 --genomeDir /home/philipp_bs/bioinf_isilon/Research/HUTTER/Internal/philipp_bioinf/singleron/hs_ensembl_110 --panel lung_1  --bam .//KM1_RNA_test/06.target_metrics/KM1_RNA_test_filtered_sorted.bam --match_dir ./result_celescope_KM1_total 
celescope snp filter_snp --outdir .//KM1_RNA_test/08.filter_snp --sample KM1_RNA_test --thread 20 --ref_threshold_method otsu --alt_threshold_method otsu --ref_min_support_read 2 --alt_min_support_read 2  --vcf .//KM1_RNA_test/07.variant_calling/KM1_RNA_test_norm.vcf 
celescope snp analysis_snp --outdir .//KM1_RNA_test/09.analysis_snp --sample KM1_RNA_test --thread 20 --database GRCh38.mane.1.0.ensembl --panel lung_1 --plot_top_n 20  --match_dir ./result_celescope_KM1_total --vcf .//KM1_RNA_test/08.filter_snp/KM1_RNA_test_filtered.vcf

Version 1.17.0

PhilippBanza avatar Sep 04 '23 09:09 PhilippBanza

It complained that the gene expression matrix directory was not found the in ./result_celescope_KM1_total/*count/

FileNotFoundError: No file found for ['./result_celescope_KM1_total/*count/*filtered_feature_bc_matrix', './result_celescope_KM1_total/*count/*matrix_10X']

Did the celescope rna pipeline complete successfully?

zhouyiqi91 avatar Sep 04 '23 09:09 zhouyiqi91