Error Messages when Running Ancestral_State_Reconstruction_Roary.py and Kp.gwas_runs.sh #2
Comments
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Hi, Thanks for using PowerBacGWAS for your research. Would you be able to share the original phylogenetic tree file (RAxML_bipartitions.bootmap) and pan-genome table (gene_presence_absence.Rtab)? I can give it a go to see if I can reproduce this error. You may also want to try using the Docker/Nextflow implementation to see if you get the same error (just to rule out dependencies issues). |
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Thanks for the quick reply! I've attached the two input files I used. As for trying the Docker/Nextflow implementation, I've been having issues with using Nextflow on our cluster. I'm trying to work through them, but needed a quicker option - which is why I opted to use the individual commands. |
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It looks as if it was not an issue with dependencies but with the format of the input file (gene_presence_absence.Rtab), specifically with the symbol ~ in the gene names which made pastml crash. After editing the input pan-genome file: |
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Great, thanks so much - that worked for the ancestral_state_reconstruction_roary.py step! It was able to produce the csv files with no error and ancestral_steps.csv had the same number of lines as the edited Rtab file. I am still having issues when running 'bash kp.gwas_runs.sh'. When I tried to run this command with the edited Rtab, I am still getting the same error messages that I had posted in my initial message. When you tried to reproduce the issue did this occur for you? I can see if I can post the full error message, however it is very lengthy and repetitive. Thanks for your help! |
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I can attempt to reproduce this issue. Can you also share the file 'paramters.binary.efs.txt' too? |
Hello,
Thank you for this tool. I am attempting to use this to do power calculations for pan-genome GWAS. These are the commands I have run:
python3 ./scripts/annotate_nodes_newick.py --input_tree RAxML_bipartitions.bootmap --output_tree tree.annotated.nwk
python3 ./scripts/roary_to_pastml_matrix.py --gene_presence_absence gene_presence_absence.Rtab --input_format 2 --output_table pastml.csv
python3 ./scripts/roary_to_plink_files.py --gene_presence_absence gene_presence_absence.Rtab --input_format 2 --output_prefix kp.pg
python3 ./scripts/ancestral_state_reconstruction_roary.py --input_pastml_table pastml.csv --input_tree tree.annotated.nwk --output_table ancestral.csv --output_steps ancestral_steps.csv --process 8 # this command produced an error
python3 ./pyseer/scripts/phylogeny_distance.py --calc-C --midpoint tree.annotated.nwk > tree_distances.csv
python3 ./scripts/prepare_gwas_runs_roary.py --roary_table gene_presence_absence.Rtab --input_format 2 --parameters_file paramters.binary.efs.txt --code_directory ./scripts/ --pyseer_path ./pyseer/pyseer-runner.py --similarity tree_distances.csv --plink_prefix kp.pg --pastml_steps_file ancestral_steps.csv --output_dir output_dir --output_prefix kp
bash kp.gwas_runs.sh
python3 ./scripts/process_gwas_runs.py --gwas_runs_in_table kp.gwas_runs.csv --variant_type r --output_dir ./output_dir/ --gwas_runs_out_table kp.ph.gwas_runs.results.csv
Rscript ./scripts/plot_gwas_runs.R --input_table kp.ph.gwas_runs.results.csv --parameters_file paramters.binary.efs.txt --plot_type 1 -v 12034 --output_plot kp.gwas_runs.results.plot.pdf
When I ran ancestral_state_reconstruction_roary.py I got some error messages about files not being found. I was still able to get the necessary outputs from this step, but I am wondering if these error messages affected the final plot. Here is the output from the command:
ancestral_state_error.txt
Additionally, when I ran 'bash kp.gwas_runs.sh' I received another set of errors. Again, the script did not exit so I was able to obtain the necessary outputs, but I am wondering what these error messages are and how they may have affected the power calculations.
This is a truncated version of the error message when running kp.gwas_runs.sh as the full output is too large. I can send you the entire error message, if necessary. Just trying to understand these errors and if/how they affect the final power calculations. Thanks!
No observations of group_5941 in selected samples
No observations of group_2493 in selected samples
10722 loaded variants
4093 pre-filtered variants
6629 tested variants
10722 printed variants
2023-02-06 11:21:04,013 INFO: Saving number of homoplasies (steps) per gene...
2023-02-06 11:21:04,016 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:04,123 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:04,123 INFO: Selecting variants meeting criteria...
2023-02-06 11:21:04,132 INFO: Selecting variants meeting criteria. DONE.
2023-02-06 11:21:04,132 INFO: Randomly sampling of variants meeting criteria.
2023-02-06 11:21:04,547 INFO: Reading causal variant file /scr1/users/theillere/usda37/powerbacgwas2/output_dir/HWFRVODMREFP.causal_variants.txt...
2023-02-06 11:21:04,548 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:04,594 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:04,594 INFO: Extracting samples with and without causal variant(s) (mutated and wild-type)...
2023-02-06 11:21:04,594 INFO: Calculating number of cases and controls, with and without the causal variant, to achieve the chosen odds ratio...
Traceback (most recent call last):
File "/scr1/users/theillere/usda37/powerbacgwas2/scripts/simulate_binary_phenotype_roary.py", line 406, in
_main()
File "/scr1/users/theillere/usda37/powerbacgwas2/scripts/simulate_binary_phenotype_roary.py", line 358, in _main
args=(len(roary_samples_mut), len(roary_samples_wt), float(args.allele_frequency), int(sample_size), float(odds_ratio)),
ValueError: could not convert string to float: 'NA'
mv: cannot stat '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/HWFRVODMREFP.phen': No such file or directory
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/HWFRVODMREFP.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/HWFRVODMREFP.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/HWFRVODMREFP.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/HWFRVODMREFP.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/HWFRVODMREFP.pyseer.phen'
2023-02-06 11:21:09,910 INFO: Saving number of homoplasies (steps) per gene...
2023-02-06 11:21:09,913 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:10,000 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:10,000 INFO: Selecting variants meeting criteria...
2023-02-06 11:21:10,009 INFO: Selecting variants meeting criteria. DONE.
2023-02-06 11:21:10,009 INFO: Randomly sampling of variants meeting criteria.
2023-02-06 11:21:10,430 INFO: Reading causal variant file /scr1/users/theillere/usda37/powerbacgwas2/output_dir/KNMUBUQIHASD.causal_variants.txt...
2023-02-06 11:21:10,431 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:10,476 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:10,476 INFO: Extracting samples with and without causal variant(s) (mutated and wild-type)...
2023-02-06 11:21:10,477 INFO: Calculating number of cases and controls, with and without the causal variant, to achieve the chosen odds ratio...
Traceback (most recent call last):
File "/scr1/users/theillere/usda37/powerbacgwas2/scripts/simulate_binary_phenotype_roary.py", line 406, in
_main()
File "/scr1/users/theillere/usda37/powerbacgwas2/scripts/simulate_binary_phenotype_roary.py", line 358, in _main
args=(len(roary_samples_mut), len(roary_samples_wt), float(args.allele_frequency), int(sample_size), float(odds_ratio)),
ValueError: could not convert string to float: 'NA'
mv: cannot stat '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/KNMUBUQIHASD.phen': No such file or directory
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/KNMUBUQIHASD.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/KNMUBUQIHASD.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/KNMUBUQIHASD.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/KNMUBUQIHASD.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/KNMUBUQIHASD.pyseer.phen'
2023-02-06 11:21:15,844 INFO: Saving number of homoplasies (steps) per gene...
2023-02-06 11:21:15,847 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:15,935 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:15,935 INFO: Selecting variants meeting criteria...
2023-02-06 11:21:15,944 INFO: Selecting variants meeting criteria. DONE.
2023-02-06 11:21:15,944 INFO: Randomly sampling of variants meeting criteria.
2023-02-06 11:21:16,354 INFO: Reading causal variant file /scr1/users/theillere/usda37/powerbacgwas2/output_dir/XPZEDQRQDHGK.causal_variants.txt...
2023-02-06 11:21:16,355 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:16,401 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:16,401 INFO: Extracting samples with and without causal variant(s) (mutated and wild-type)...
2023-02-06 11:21:16,401 INFO: Calculating number of cases and controls, with and without the causal variant, to achieve the chosen odds ratio...
Traceback (most recent call last):
File "/scr1/users/theillere/usda37/powerbacgwas2/scripts/simulate_binary_phenotype_roary.py", line 406, in
_main()
File "/scr1/users/theillere/usda37/powerbacgwas2/scripts/simulate_binary_phenotype_roary.py", line 358, in _main
args=(len(roary_samples_mut), len(roary_samples_wt), float(args.allele_frequency), int(sample_size), float(odds_ratio)),
ValueError: could not convert string to float: 'NA'
mv: cannot stat '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/XPZEDQRQDHGK.phen': No such file or directory
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/XPZEDQRQDHGK.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/XPZEDQRQDHGK.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/XPZEDQRQDHGK.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/XPZEDQRQDHGK.pyseer.phen'
Traceback (most recent call last):
File "./pyseer/pyseer-runner.py", line 8, in
main()
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/main.py", line 305, in main
p = load_phenotypes(options.phenotypes, options.phenotype_column)
File "/scr1/users/theillere/usda37/powerbacgwas2/pyseer/pyseer/input.py", line 37, in load_phenotypes
p = pd.read_csv(infile, index_col=0, sep='\t')
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init
self._make_engine(self.engine)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/theillere/miniconda3/envs/powerbacgwas/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/theillere/usda37/powerbacgwas2/output_dir/XPZEDQRQDHGK.pyseer.phen'
2023-02-06 11:21:21,694 INFO: Saving number of homoplasies (steps) per gene...
2023-02-06 11:21:21,698 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:21,786 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:21,786 INFO: Selecting variants meeting criteria...
2023-02-06 11:21:21,795 INFO: Selecting variants meeting criteria. DONE.
2023-02-06 11:21:21,795 INFO: Randomly sampling of variants meeting criteria.
2023-02-06 11:21:22,211 INFO: Reading causal variant file /scr1/users/theillere/usda37/powerbacgwas2/output_dir/NRRUMMWMXBFS.causal_variants.txt...
2023-02-06 11:21:22,212 INFO: Opening gene_presence_absence.Rtab file and calculating gene frequency...
2023-02-06 11:21:22,257 INFO: Opening gene_presence_absence file and calculating gene frequency. DONE.
2023-02-06 11:21:22,257 INFO: Extracting samples with and without causal variant(s) (mutated and wild-type)...
2023-02-06 11:21:22,258 INFO: Calculating number of cases and controls, with and without the causal variant, to achieve the chosen odds ratio...
The text was updated successfully, but these errors were encountered: