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.
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.
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.