To whom it concerns,

When I tried to run the Strtrak for demo, there are some issues occurred.

The command showed below: ./StrTrak base -i Streptococcus.USCG_test.txt -p Streptococcus.USCG_test

Issues listed below:

Running /home/wuzq-cdc/miniconda3/envs/strtrak/bin/bindash commit -clean Reading input filenames from reference.list. Unable to open the file GCF_003086355.fna.gz Running /home/wuzq-cdc/miniconda3/envs/strtrak/bin/bindash commit -clean Error: cannot open the file reference for reading Traceback (most recent call last): File "/home/wuzq-cdc/tools/StrTrak/test/../StrTrak", line 63, in cli() File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/tools/StrTrak/test/../StrTrak", line 42, in base strBase.strBase(fna_list, min_dist, min_cov, prefix, threads) File "/home/wuzq-cdc/tools/StrTrak/strBase.py", line 221, in strBase representatives = get_representative(references, threads, tmpdir, min_dist) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/tools/StrTrak/strBase.py", line 180, in get_representative data = pd.read_csv(os.path.join(tmpdir, 'reference.dist'), sep='\t', dtype=str) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 620, in _read parser = TextFileReader(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1620, in init self._engine = self._make_engine(f, self.engine) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine self.handles = get_handle( ^^^^^^^^^^^ File "/home/wuzq-cdc/miniconda3/envs/strtrak/lib/python3.11/site-packages/pandas/io/common.py", line 873, in get_handle handle = open( ^^^^^ FileNotFoundError: [Errno 2] No such file or directory: './tmp7wts992a/reference.dist'

Best, Bruce