Empty Output Directories
Created by: chandnisidhu
Hi,
I have used my metagenomic data to check this pipeline. The pipeline worked well but the output directories generated were empty with no information. Please look into the matter.
nbhb-001-017:MOSCA-master csid$ python main.py --files /Users/csid/Documents/SRP187387_1.fastq /Users/csidhu/Documents/SRP187387_2 -o /Users/csid/Documents/ { 'annotation_database': 'Databases/Annotation/uniprot.dmnd', 'assembler': 'metaspades', 'conditions': None, 'files': [ '/Users/csid/Documents/SRP187387_1.fastq', '/Users/csid/Documents/SRP187387_2'], 'metaproteomic': False, 'no_annotation': False, 'no_assembly': False, 'no_binning': False, 'no_preprocessing': False, 'output': '/Users/csid/Documents', 'output_level': 'min', 'type_of_data': 'paired'}
{'files': ['/Users/csid/Documents/SRP187387_1.fastq', '/Users/csid/Documents/SRP187387_2'], 'type_of_data': 'paired', 'assembler': 'metaspades', 'annotation_database': 'Databases/Annotation/uniprot.dmnd', 'output': '/Users/csidhu/Documents', 'no_preprocessing': False, 'no_assembly': False, 'no_annotation': False, 'no_binning': False, 'output_level': 'min', 'metaproteomic': False, 'conditions': None} Files Experiment1 MG files: /Users/csid/Documents/SRP187387_1.fastq Experiment2 MG files: /Users/csid/Documents/SRP187387_2 Type of data: paired Assembler: metaspades Annotation database: Databases/Annotation/uniprot.dmnd Output: /Users/csid/Documents No preprocessing: False No assembly: False No annotation: False No binning: False Output level: min Metaproteomic: False Conditions: None Creating directories at /Users/csid/Documents Created /Users/csid/Documents/Preprocess/FastQC Created /Users/csid/Documents/Preprocess/Trimmomatic Created /Users/csid/Documents/Preprocess/SortMeRNA Created /Users/csid/Documents/Assembly Created /Users/csid/Documents/Annotation Created /Users/csid/Documents/Metatranscriptomics_analysis Splitting reads in /Users/csid/Documents/SRP187387_1.fastq to /Users/csid/Documents/Preprocess/SRP187387_1_R1.fastq and /Users/csid/Documents/Preprocess/SRP187387_1_R2.fastq. Handling SRP187387_1 Preprocessing of metagenomic reads has begun Assembly has begun Annotation has begun Binning has begun Splitting reads in /Users/csid/Documents/SRP187387_2 to /Users/csid/Documents/Preprocess/SRP187387_2_R1.fastq and /Users/csid/Documents/Preprocess/SRP187387_2_R2.fastq. Handling SRP187387_2 Preprocessing of metagenomic reads has begun Assembly has begun Annotation has begun Binning has begun nbhb-001-017:MOSCA-master csid$