File not found error
Created by: MingL196
Hi,
I tried running MOSCA using the command:
python MOSCA/scripts/mosca.py --files /hpc/home/mzl5860/Ming_workdir/G549/MOSCA/files_rename/G549-01-R1.fastq.gz,/hpc/home/mzl5860/Ming_workdir/G549/MOSCA/files_rename/G549-01-R2.fastq.gz --output output
The program ran up the FASTQC step, but then returned the error:
Traceback (most recent call last):
File "MOSCA/scripts/mosca.py", line 170, in
reporter.info_from_preprocessing(args.output, mg_name, mg[0])
File "/ri/shared/modules7/miniconda3/envs/mosca-1.0.2/MOSCA/scripts/report.py", line 112, in info_from_preprocessing
self.info_from_fastqc(output_dir, name, '[Initial quality assessment]', prefix2terms)
File "/ri/shared/modules7/miniconda3/envs/mosca-1.0.2/MOSCA/scripts/report.py", line 76, in info_from_fastqc
prefix2terms[prefix][0], name, prefix2terms[prefix][i])) for i in [1, 2]]
File "/ri/shared/modules7/miniconda3/envs/mosca-1.0.2/MOSCA/scripts/report.py", line 76, in
prefix2terms[prefix][0], name, prefix2terms[prefix][i])) for i in [1, 2]]
File "/ri/shared/modules7/miniconda3/envs/mosca-1.0.2/MOSCA/scripts/mosca_tools.py", line 584, in parse_fastqc_report
file = open(filename).read().split('\n')
FileNotFoundError: [Errno 2] No such file or directory: 'output/Preprocess/FastQC/G549-01-R1.fastq.gz_R1_fastqc/fastqc_data.txt'
The program seems to be trying to read from the wrong file. Is there some format that the file names need to be in?
Can this be fixed?
Thanks.