tbrunetti / quack Goto Github PK

Syntax errors in run_GWAS_QC_filtering_pipeline.py and generate_report.py -- additional commas causing problems

Hi all,
I'm a biologist learning bioinformatics.
Trying to run the pipeline I have this error when running Basic Mode example:

**chunky run run_GWAS_QC_filtering_pipeline.py -sampleTable /home/usuario/my_project/GWAS_QC_pipeline/SampleTable.txt -snpTable /home/usuario/my_project/GWAS_QC_pipeline/SNPTable.txt -inputPLINK /home/usuario/my_project/GWAS_QC_pipeline/toy.ped**

Does anybody could help to find the problem? It is a common one?
I followed the readme instructions step by step and everything was correct. All programs and dependencies and files are in the same folder.
Thank you in advance and congrats for the pipeline!

Pelayo

Traceback (most recent call last):
File "/home/usuario/miniconda2/lib/python2.7/site-packages/chunkypipes/util/init.py", line 74, in execute_from_command_line
chunky_command_classes[subcommand].run(argv[2:])
File "/home/usuario/miniconda2/lib/python2.7/site-packages/chunkypipes/util/commands/run.py", line 44, in run
pipeline_config=pipeline_class.pipeline_config
File "/home/usuario/miniconda2/lib/python2.7/site-packages/chunkypipes/components/init.py", line 467, in _run_pipeline
self.run_pipeline(pipeline_args=pipeline_args, pipeline_config=pipeline_config)
File "run_GWAS_QC_filtering_pipeline.py", line 345, in run_pipeline
inputPlinkfile=pipeline_args['inputPLINK'], plink=pipeline_config['plink']['path']
File "run_GWAS_QC_filtering_pipeline.py", line 59, in check_input_format
convert = subprocess.call([str(plink), '--file', str(inputPlinkfile[:-4]), '--make-bed', '--out', str(inputPlinkfile[:-4])])
File "/home/usuario/miniconda2/lib/python2.7/subprocess.py", line 172, in call
return Popen(*popenargs, **kwargs).wait()
File "/home/usuario/miniconda2/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/home/usuario/miniconda2/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory