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staphopia / staphopia-sccmec

A standalone version of Staphopia's SCCmec typing method.
MIT License
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problem with the data path to run --test #10

Open ariasamin opened 1 year ago

ariasamin commented 1 year ago

I am delighted to find out a specific genome analysis software for Staphylococcus aureus. I appreciate it. I have installed the software in zfs, and apparently, it has been installed correctly.

(/*/*/bin/env/staphopia_sccmec_env) [*@node1119 staphopia]$ conda activate /*/*/bin/env/staphopia_sccmec_env
(/*/*/bin/env/staphopia_sccmec_env) [*@node1119 staphopia]$ staphopia-sccmec
usage: staphopia-sccmec [-h] [--assembly ASSEMBLY|ASSEMBLY_DIR|STAPHOPIA_DIR] [--staphopia STAPHOPIA_DIR] [--sccmec SCCMEC_DATA] [--ext STR] [--hamming]
                        [--json] [--debug] [--depends] [--test] [--citation] [--version]

Determine SCCmec Type/SubType

options:
  -h, --help            show this help message and exit

Options:

  --assembly ASSEMBLY|ASSEMBLY_DIR|STAPHOPIA_DIR
                        Input assembly (FASTA format), directory of assemblies to predict SCCmec. (Cannot be used with --staphopia)
  --staphopia STAPHOPIA_DIR
                        Input directory of samples processed by Staphopia. (Cannot be used with --assembly)
  --sccmec SCCMEC_DATA  Directory where SCCmec reference data is stored (Default: /*/*/env/staphopia_sccmec_env/share/staphopia-sccmec/data).
  --ext STR             Extension used by assemblies. (Default: fna)
  --hamming             Report the hamming distance of each type.
  --json                Report the output as JSON (Default: tab-delimited)
  --debug               Print debug related text.
  --depends             Verify dependencies are installed/found.
  --test                Run with example test data.
  --citation            Print citation information for using Staphopia SCCmec
  --version             show program's version number and exit

However, when running --test / --depends, an error comes up referring to the path. I wonder why it uses a wrong path by ignoring the "bin" the path should be ///bin/env/staphopia_sccmec_env, however it has been changed to ///env/staphopia_sccmec_env. Would you please help me with this? Thank you. 

(/*/*/bin/env/staphopia_sccmec_env) [*@node1119 staphopia]$ staphopia-sccmec --test
2023-06-16 02:14:17:root:ERROR - primers (/*/*/env/staphopia_sccmec_env/share/staphopia-sccmec/data/primers.fasta) not found, please verify path.
2023-06-16 02:14:17:root:ERROR - subtypes (/*/*/env/staphopia_sccmec_env/share/staphopia-sccmec/data/subtypes.fasta) not found, please verify path.
2023-06-16 02:14:17:root:ERROR - Dataset requirement missing, exiting

(/*/*/bin/env/staphopia_sccmec_env) [*@node1119 staphopia]$ staphopia-sccmec --depends
2023-06-16 02:21:48:root:INFO - makeblastdb: command found!
2023-06-16 02:21:48:root:INFO - blastn: command found!
2023-06-16 02:21:48:root:ERROR - primers (/*/*/env/staphopia_sccmec_env/share/staphopia-sccmec/data/primers.fasta) not found, please verify path.
2023-06-16 02:21:48:root:ERROR - subtypes (/*/*/env/staphopia_sccmec_env/share/staphopia-sccmec/data/subtypes.fasta) not found, please verify path.
2023-06-16 02:21:48:root:ERROR - Dataset requirement missing, exiting