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2025-11-22 16:33:09,502 [INFO] logging with MIN Level >>> INFO at /home/propenster/src/wexygen/app.log
2025-11-22 16:33:09,505 [INFO] Hello.................
2025-11-22 16:33:09,507 [INFO] Welcome to the preprocessor.py...Let's create necessary files and configurations for this workflow to run successfully!
2025-11-22 16:33:09,508 [INFO] Purging output directory before processing >>> /home/propenster/src/wexygen/test/output
2025-11-22 16:33:09,511 [INFO] Output directory ready for processing >>> /home/propenster/src/wexygen/test/output
2025-11-22 16:33:09,511 [INFO] Parsing samples out of raw data path /home/propenster/src/wexygen/test/raw_data
2025-11-22 16:33:09,512 [INFO] Extracting samples from raw_data >>> SampleA_S1_L001_R2_001.fastq.gz
2025-11-22 16:33:09,512 [INFO] Recognizing file naming patterns
2025-11-22 16:33:09,512 [INFO] Sample pattern info recognized from file: SampleA_S1_L001_R2_001.fastq.gz >>> {'file_name': 'SampleA_S1_L001_R2_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R2', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None}
2025-11-22 16:33:09,513 [INFO] Extracting samples from raw_data >>> SampleA_S1_L001_R1_001.fastq.gz
2025-11-22 16:33:09,513 [INFO] Recognizing file naming patterns
2025-11-22 16:33:09,513 [INFO] Sample pattern info recognized from file: SampleA_S1_L001_R1_001.fastq.gz >>> {'file_name': 'SampleA_S1_L001_R1_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R1', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None}
2025-11-22 16:33:09,514 [INFO] Samples parsed out to be converted to data frame defaultdict(<class 'dict'>, {'SampleA': {'file_name': 'SampleA_S1_L001_R1_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R1', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None, 'file2': 'SampleA_S1_L001_R2_001.fastq.gz', 'PE': True}})
2025-11-22 16:33:09,528 [INFO] Checking sample file patterns is consistent and unique
2025-11-22 16:33:09,529 [INFO] Checking sample file patterns is consistent and unique
2025-11-22 16:33:09,529 [INFO] Exporting sample data frame into /home/propenster/src/wexygen/test/output/samples.tsv
2025-11-22 17:22:30,890 [INFO] logging with MIN Level >>> INFO at /home/propenster/src/wexygen/app.log
2025-11-22 17:22:30,894 [INFO] Hello.................
2025-11-22 17:22:30,897 [INFO] Welcome to the preprocessor.py...Let's create necessary files and configurations for this workflow to run successfully!
2025-11-22 17:22:30,899 [INFO] Purging output directory before processing >>> /home/propenster/src/wexygen/test/output
2025-11-22 17:22:30,903 [INFO] Output directory ready for processing >>> /home/propenster/src/wexygen/test/output
2025-11-22 17:22:30,903 [INFO] Parsing samples out of raw data path /home/propenster/src/wexygen/test/raw_data
2025-11-22 17:22:30,904 [INFO] Extracting samples from raw_data >>> SampleA_S1_L001_R2_001.fastq.gz
2025-11-22 17:22:30,904 [INFO] Recognizing file naming patterns
2025-11-22 17:22:30,905 [INFO] Sample pattern info recognized from file: SampleA_S1_L001_R2_001.fastq.gz >>> {'file_name': 'SampleA_S1_L001_R2_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R2', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None}
2025-11-22 17:22:30,906 [INFO] Extracting samples from raw_data >>> SampleA_S1_L001_R1_001.fastq.gz
2025-11-22 17:22:30,906 [INFO] Recognizing file naming patterns
2025-11-22 17:22:30,906 [INFO] Sample pattern info recognized from file: SampleA_S1_L001_R1_001.fastq.gz >>> {'file_name': 'SampleA_S1_L001_R1_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R1', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None}
2025-11-22 17:22:30,907 [INFO] Samples parsed out to be converted to data frame defaultdict(<class 'dict'>, {'SampleA': {'file_name': 'SampleA_S1_L001_R1_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R1', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None, 'file2': 'SampleA_S1_L001_R2_001.fastq.gz', 'PE': True}})
2025-11-22 17:22:30,918 [INFO] Checking sample file patterns is consistent and unique
2025-11-22 17:22:30,919 [INFO] Checking sample file patterns is consistent and unique
2025-11-22 17:22:30,919 [INFO] Exporting sample data frame into /home/propenster/src/wexygen/test/output/samples.tsv
2025-11-22 17:23:26,820 [INFO] Parsed command line args input dir >>> /home/propenster/src/wexygen/test/raw_data output dir >>> /home/propenster/src/wexygen/test/output
2025-11-22 17:23:26,821 [INFO] Starting to preprocess parsed cmd args
2025-11-22 17:23:26,821 [INFO] Checking if Work Directory (Output Dir) exists at /home/propenster/src/wexygen/test/output
2025-11-22 17:23:26,821 [INFO] Parsing config files from preprocessor >>> /home/propenster/src/wexygen/test/output/all_args.json
2025-11-22 17:23:26,822 [INFO] Writing args to yaml config >>> /home/propenster/src/wexygen/test/output/config.yaml
2025-11-22 17:23:26,823 [INFO] Arguments written to YAML config >>> /home/propenster/src/wexygen/test/output/config.yaml
2025-11-22 17:23:26,823 [INFO] --use-snakemake is enabled running workflows with snakemake
2025-11-22 17:23:26,823 [INFO] Snakemake command constructed >>> snakemake --snakefile '/home/propenster/src/wexygen/workflow/Snakefile' --configfile '/home/propenster/src/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/wexygen/test/output/WES_sample_snakemake_flow.png'
2025-11-22 17:23:26,824 [INFO] Running snakemake workflow now at 2025-11-22 17:23:26,824
2025-11-22 18:02:24,285 [INFO] Parsed command line args input dir >>> '/home/propenster/src/wexygen/test/raw_data' output dir >>> '/home/propenster/src/wexygen/test/output'
2025-11-22 18:02:24,287 [INFO] Starting to preprocess parsed cmd args
2025-11-22 18:02:24,287 [INFO] Checking if Work Directory (Output Dir) exists at '/home/propenster/src/wexygen/test/output'
2025-11-22 18:02:24,288 [INFO] Parsing config files from preprocessor >>> '/home/propenster/src/wexygen/test/output/all_args.json'
2025-11-22 18:02:24,289 [INFO] Writing args to yaml config >>> '/home/propenster/src/wexygen/test/output/config.yaml'
2025-11-22 18:02:24,289 [INFO] Arguments written to YAML config >>> '/home/propenster/src/wexygen/test/output/config.yaml'
2025-11-22 18:02:24,290 [INFO] --use-snakemake is enabled running workflows with snakemake
2025-11-22 18:02:24,290 [INFO] Snakemake command constructed >>> snakemake --snakefile '/home/propenster/src/wexygen/workflow/Snakefile' --configfile '/home/propenster/src/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/wexygen/test/output/WES_sample_snakemake_flow.png'
2025-11-22 18:02:24,290 [INFO] Running snakemake workflow now at 2025-11-22 18:02:24,290
2025-11-22 21:12:08,922 [INFO] Parsed command line args input dir >>> '/home/propenster/src/wexygen/test/raw_data' output dir >>> '/home/propenster/src/wexygen/test/output'
2025-11-22 21:12:08,924 [INFO] Starting to preprocess parsed cmd args
2025-11-22 21:12:08,924 [INFO] Checking if Work Directory (Output Dir) exists at '/home/propenster/src/wexygen/test/output'
2025-11-22 21:12:08,924 [INFO] Parsing config files from preprocessor >>> '/home/propenster/src/wexygen/test/output/all_args.json'
2025-11-22 21:12:08,925 [INFO] Writing args to yaml config >>> '/home/propenster/src/wexygen/test/output/config.yaml'
2025-11-22 21:12:08,926 [INFO] Arguments written to YAML config >>> '/home/propenster/src/wexygen/test/output/config.yaml'
2025-11-22 21:12:08,926 [INFO] --use-snakemake is enabled running workflows with snakemake
2025-11-22 21:12:08,926 [INFO] Snakemake command constructed >>> snakemake --snakefile '/home/propenster/src/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/wexygen/test/output/WES_sample_snakemake_flow.png'
2025-11-22 21:12:08,926 [INFO] Running snakemake workflow now at 2025-11-22 21:12:08,926
2025-11-22 21:15:10,445 [INFO] Running new 'WES' workflow
2025-11-22 21:15:10,446 [INFO] Parsed command line args input dir >>> '/home/propenster/src/wexygen/test/raw_data' output dir >>> '/home/propenster/src/wexygen/test/output'
2025-11-22 21:15:10,446 [INFO] Starting to preprocess parsed cmd args
2025-11-22 21:15:10,446 [INFO] Checking if Work Directory (Output Dir) exists at '/home/propenster/src/wexygen/test/output'
2025-11-22 21:15:10,447 [INFO] Parsing config files from preprocessor >>> '/home/propenster/src/wexygen/test/output/all_args.json'
2025-11-22 21:15:10,447 [INFO] Writing args to yaml config >>> '/home/propenster/src/wexygen/test/output/config.yaml'
2025-11-22 21:15:10,448 [INFO] Arguments written to YAML config >>> '/home/propenster/src/wexygen/test/output/config.yaml'
2025-11-22 21:15:10,449 [INFO] --use-snakemake is enabled running workflows with snakemake
2025-11-22 21:15:10,450 [INFO] Snakemake command constructed >>> snakemake --snakefile '/home/propenster/src/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/wexygen/test/output/WES_sample_snakemake_flow.png'
2025-11-22 21:15:10,451 [INFO] Running snakemake workflow now at 2025-11-22 21:15:10,451
2025-11-24 10:01:02,852 [INFO] Running new 'WES' workflow
2025-11-24 10:01:02,853 [INFO] Parsed command line args input dir >>> '/home/propenster/src/compbio/wexygen/test/raw_data' output dir >>> '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:01:02,853 [INFO] Starting to preprocess parsed cmd args
2025-11-24 10:01:02,853 [INFO] Checking if Work Directory (Output Dir) exists at '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:01:02,855 [INFO] Parsing config files from preprocessor >>> '/home/propenster/src/compbio/wexygen/test/output/all_args.json'
2025-11-24 10:01:02,855 [ERROR] Error parsing JSON. input dir mismatch. Ensure input specified for preprocessing is the same for execution /home/propenster/src/compbio/wexygen/test/raw_data is not same as /home/propenster/src/wexygen/test/raw_data
2025-11-24 10:01:46,840 [INFO] logging with MIN Level >>> INFO at /home/propenster/src/compbio/wexygen/app.log
2025-11-24 10:01:46,843 [INFO] Hello.................
2025-11-24 10:02:10,871 [INFO] logging with MIN Level >>> INFO at /home/propenster/src/compbio/wexygen/app.log
2025-11-24 10:02:10,873 [INFO] Hello.................
2025-11-24 10:02:10,875 [INFO] Welcome to the preprocessor.py...Let's create necessary files and configurations for this workflow to run successfully!
2025-11-24 10:02:10,876 [INFO] Purging output directory before processing >>> '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:02:10,879 [INFO] Output directory ready for processing >>> '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:02:10,879 [INFO] Parsing samples out of raw data path '/home/propenster/src/compbio/wexygen/test/raw_data'
2025-11-24 10:02:10,880 [INFO] Extracting samples from raw_data >>> SampleA_S1_L001_R2_001.fastq.gz
2025-11-24 10:02:10,880 [INFO] Recognizing file naming patterns
2025-11-24 10:02:10,880 [INFO] Sample pattern info recognized from file: 'SampleA_S1_L001_R2_001.fastq.gz' >>> {'file_name': 'SampleA_S1_L001_R2_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R2', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None}
2025-11-24 10:02:10,880 [INFO] Extracting samples from raw_data >>> SampleA_S1_L001_R1_001.fastq.gz
2025-11-24 10:02:10,881 [INFO] Recognizing file naming patterns
2025-11-24 10:02:10,881 [INFO] Sample pattern info recognized from file: 'SampleA_S1_L001_R1_001.fastq.gz' >>> {'file_name': 'SampleA_S1_L001_R1_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R1', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None}
2025-11-24 10:02:10,881 [INFO] Samples parsed out to be converted to data frame defaultdict(<class 'dict'>, {'SampleA': {'file_name': 'SampleA_S1_L001_R1_001.fastq.gz', 'matched_pattern': 'illumina', 'sample_name': 'SampleA', 'sample_id': 'S1', 'read_num': 'R1', 'lane': 'L001', 'tail': '001', 'ext': 'fastq.gz', 'unit': None, 'file2': 'SampleA_S1_L001_R2_001.fastq.gz', 'PE': True}})
2025-11-24 10:02:10,892 [INFO] Checking sample file patterns is consistent and unique
2025-11-24 10:02:10,894 [INFO] Checking sample file patterns is consistent and unique
2025-11-24 10:02:10,895 [INFO] Exporting sample data frame into '/home/propenster/src/compbio/wexygen/test/output/samples.tsv'
2025-11-24 10:02:10,901 [INFO] Writing config to json in output path >>> '/home/propenster/src/compbio/wexygen/test/output/all_args.json'
2025-11-24 10:02:20,559 [INFO] Running new 'WES' workflow
2025-11-24 10:02:20,560 [INFO] Parsed command line args input dir >>> '/home/propenster/src/compbio/wexygen/test/raw_data' output dir >>> '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:02:20,560 [INFO] Starting to preprocess parsed cmd args
2025-11-24 10:02:20,560 [INFO] Checking if Work Directory (Output Dir) exists at '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:02:20,560 [INFO] Parsing config files from preprocessor >>> '/home/propenster/src/compbio/wexygen/test/output/all_args.json'
2025-11-24 10:02:20,561 [INFO] Writing args to yaml config >>> '/home/propenster/src/compbio/wexygen/test/output/config.yaml'
2025-11-24 10:02:20,561 [INFO] Arguments written to YAML config >>> '/home/propenster/src/compbio/wexygen/test/output/config.yaml'
2025-11-24 10:02:20,561 [INFO] --use-snakemake is enabled running workflows with snakemake
2025-11-24 10:02:20,561 [INFO] Snakemake command constructed >>> snakemake --snakefile '/home/propenster/src/compbio/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/compbio/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/compbio/wexygen/test/output/WES_sample_snakemake_flow.png'
2025-11-24 10:02:20,561 [INFO] Running snakemake workflow with command snakemake --snakefile '/home/propenster/src/compbio/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/compbio/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/compbio/wexygen/test/output/WES_sample_snakemake_flow.png' now at 2025-11-24 10:02:20,561
2025-11-24 10:30:51,075 [INFO] Running new 'WES' workflow
2025-11-24 10:30:51,076 [INFO] Parsed command line args input dir >>> '/home/propenster/src/compbio/wexygen/test/raw_data' output dir >>> '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:30:51,076 [INFO] Starting to preprocess parsed cmd args
2025-11-24 10:30:51,076 [INFO] Checking if Work Directory (Output Dir) exists at '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:30:51,076 [INFO] Parsing config files from preprocessor >>> '/home/propenster/src/compbio/wexygen/test/output/all_args.json'
2025-11-24 10:30:51,077 [INFO] Writing args to yaml config >>> '/home/propenster/src/compbio/wexygen/test/output/config.yaml'
2025-11-24 10:30:51,078 [INFO] Arguments written to YAML config >>> '/home/propenster/src/compbio/wexygen/test/output/config.yaml'
2025-11-24 10:30:51,078 [INFO] --use-snakemake is enabled running workflows with snakemake
2025-11-24 10:30:51,078 [INFO] Snakemake command constructed >>> snakemake --snakefile '/home/propenster/src/compbio/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/compbio/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/compbio/wexygen/test/output/WES_sample_snakemake_flow.png'
2025-11-24 10:30:51,078 [INFO] Running snakemake workflow with command snakemake --snakefile '/home/propenster/src/compbio/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/compbio/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/compbio/wexygen/test/output/WES_sample_snakemake_flow.png' now at 2025-11-24 10:30:51,078
2025-11-24 10:30:51,424 [ERROR] stdout: sh: 1: snakemake: not found
2025-11-24 10:36:16,930 [INFO] Running new 'WES' workflow
2025-11-24 10:36:16,930 [INFO] Parsed command line args input dir >>> '/home/propenster/src/compbio/wexygen/test/raw_data' output dir >>> '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:36:16,930 [INFO] Starting to preprocess parsed cmd args
2025-11-24 10:36:16,930 [INFO] Checking if Work Directory (Output Dir) exists at '/home/propenster/src/compbio/wexygen/test/output'
2025-11-24 10:36:16,931 [INFO] Parsing config files from preprocessor >>> '/home/propenster/src/compbio/wexygen/test/output/all_args.json'
2025-11-24 10:36:16,931 [INFO] Writing args to yaml config >>> '/home/propenster/src/compbio/wexygen/test/output/config.yaml'
2025-11-24 10:36:16,932 [INFO] Arguments written to YAML config >>> '/home/propenster/src/compbio/wexygen/test/output/config.yaml'
2025-11-24 10:36:16,932 [INFO] --use-snakemake is enabled running workflows with snakemake
2025-11-24 10:36:16,932 [INFO] Snakemake command constructed >>> snakemake --snakefile '/home/propenster/src/compbio/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/compbio/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/compbio/wexygen/test/output/WES_sample_snakemake_flow.png'
2025-11-24 10:36:16,932 [INFO] Running snakemake workflow with command snakemake --snakefile '/home/propenster/src/compbio/wexygen/workflow_files/snakemake/Snakefile' --configfile '/home/propenster/src/compbio/wexygen/test/output/config.yaml' -j 12 --rulegraph | dot -Tpng > '/home/propenster/src/compbio/wexygen/test/output/WES_sample_snakemake_flow.png' now at 2025-11-24 10:36:16,932
2025-11-24 10:36:17,360 [ERROR] sh: 1: snakemake: not found