Error while running 3Call_sv_to_genotype.py

[shengpeng1996]

Hello, I got the following error when running the 3Call_sv_to_genotype.py script. I don’t know what caused it. hash-3.0.1 provided by Decision Patterns

Loading required package: snow

Attaching package: ‘snow’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
parCapply, parLapply, parRapply, parSapply, splitIndices,
stopCluster

Error in .set(h, keys = file_name, values = read.table(file = paste(depthfile_dir, : could not find function ".set" Execution halted Traceback (most recent call last): File "/data/shengp/analysis_scripts/psvcp_v1.01/example7/../structure_variation_calling_script/3.1pav_genotype_to_hmp.py", line 8, in df = pd.read_csv(sys.argv[1],sep='\t') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/software/anaconda3/envs/psvcp/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/software/anaconda3/envs/psvcp/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 620, in _read parser = TextFileReader(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/software/anaconda3/envs/psvcp/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1620, in init self._engine = self._make_engine(f, self.engine) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/software/anaconda3/envs/psvcp/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine return mapping[engine](f, self.options) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/software/anaconda3/envs/psvcp/lib/python3.12/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init self._reader = parsers.TextReader(src, **kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file Traceback (most recent call last): File "/data/shengp/analysis_scripts/psvcp_v1.01/example7/../structure_variation_calling_script/3.2hapmap_screen_maf.py", line 6, in hmp = open(sys.argv[1],'r') ^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'hmp_prefix.hmp'

Thank you very much