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492
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1 # Troubleshooting
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2
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3 Common issues and solutions when using COBRAxy.
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4
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5 ## Installation Issues
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6
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542
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7 ### Missing Build Tools
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8
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9 **Problem**: `gcc: command not found` or compilation errors (Linux/macOS)
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10 ```bash
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11 # Ubuntu/Debian
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12 sudo apt-get install build-essential cmake pkg-config
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13
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14 # macOS
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15 xcode-select --install
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16 brew install cmake pkg-config
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17 ```
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18
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19 **Problem**: `CMake not found`
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20 ```bash
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21 # Ubuntu/Debian
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22 sudo apt-get install cmake
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23
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24 # macOS
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25 brew install cmake
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26
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27 # Or via conda
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28 conda install -c conda-forge cmake
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29 ```
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30
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492
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31 ### Python Import Errors
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32
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33 **Problem**: `ModuleNotFoundError: No module named 'cobra'`
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34 ```bash
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542
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35 # Solution: Reinstall COBRAxy with dependencies
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36 cd COBRAxy/src
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37 pip install .
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38
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542
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39 # Or install missing dependency directly
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40 pip install cobra
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492
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41 ```
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42
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43 **Problem**: `ImportError: No module named 'cobraxy'`
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44 ```python
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542
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45 # Solution: Ensure COBRAxy is installed
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46 pip install /path/to/COBRAxy/src/
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47
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48 # Or add to Python path temporarily
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492
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49 import sys
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542
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50 sys.path.insert(0, '/path/to/COBRAxy/src')
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492
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51 ```
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52
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53 ### System Dependencies
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54
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55 **Problem**: GLPK solver not found
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56 ```bash
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57 # Ubuntu/Debian
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58 sudo apt-get install libglpk40 glpk-utils
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59 pip install swiglpk
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60
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61 # macOS
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62 brew install glpk
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63 pip install swiglpk
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64
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65 # Windows (using conda)
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66 conda install -c conda-forge glpk swiglpk
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67 ```
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68
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69
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550
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70 ## Galaxy Tool Issues
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492
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71
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550
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72 ### Import Metabolic Model
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492
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73
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550
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74 **Error message**:
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492
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75 ```bash
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550
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76 Traceback (most recent call last):
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77 File "/export/tool_deps/_conda/envs/mulled-v1-d3fef6bda7daedb89425f527672b54ab0a4be6cfe3c8725b7f8c0948e0c80773/lib/python3.11/site-packages/cobra/io/sbml.py", line 458, in read_sbml_model
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78 return _sbml_to_model(doc, number=number, f_replace=f_replace, **kwargs)
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79 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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80 File "/export/tool_deps/_conda/envs/mulled-v1-d3fef6bda7daedb89425f527672b54ab0a4be6cfe3c8725b7f8c0948e0c80773/lib/python3.11/site-packages/cobra/io/sbml.py", line 563, in _sbml_to_model
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81 raise CobraSBMLError("No SBML model detected in file.")
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82 cobra.io.sbml.CobraSBMLError: No SBML model detected in file.
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492
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83 ```
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84
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550
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85 **Meaning:**
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86 The Import Metabolic Model tool cannot read the input file as a valid SBML model with FBC annotations.
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492
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87
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550
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88 **Suggested Action:**
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89 Verify that the input XML file is in proper SBML format and includes all necessary FBC annotations.
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90
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91
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550
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92 ### Flux simulation
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492
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93
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550
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94 **Error message**:
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95 ```bash
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96 Execution aborted: wrong format of bounds dataset
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492
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97 ```
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98
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99 **Meaning:**
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100 Flux simulation cannot read the bounds of the metabolic model for the constrained simulation problem (optimization or sampling).
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101 This usually happens if the input “Bound file(s): *” is incorrect. For example, it occurs when the **RasToBounds - Cell Class** file is passed instead of the collection of bound files named **"RAS to bounds"**.
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102
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550
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103 **Suggested Action:**
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104 Check the input files and ensure the correct bounds collection is used.
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492
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105
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106 ## Getting Help
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107
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108 ### Information to Include in Bug Reports
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109
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110 When reporting issues, include:
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111
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112 1. **System information**:
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113 ```bash
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114 python --version
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115 pip list | grep cobra
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116 uname -a # Linux/macOS
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117 ```
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118
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119 2. **Complete error messages**: Copy full traceback
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120 3. **Input file format**: First few lines of input data
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121 4. **Command/parameters used**: Exact command or Python code
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122 5. **Expected vs actual behavior**: What should happen vs what happens
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123
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124 ### Community Resources
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125
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126 - **GitHub Issues**: [Report bugs and ask questions](https://github.com/CompBtBs/COBRAxy/issues)
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127 - **COBRApy Community**: [General metabolic modeling help](https://github.com/opencobra/cobrapy)
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128
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129 ### Self-Help Checklist
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130
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131 Before reporting issues:
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132
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547
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133 - Checked this troubleshooting guide
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134 - Verified installation completeness
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135 - Tested with built-in example data
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136 - Searched existing GitHub issues
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137 - Tried alternative models/parameters
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138 - Checked file formats and permissions
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139
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140
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550
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141 This troubleshooting guide covers the most common issues. For tool-specific problems, check the individual tool documentation pages.
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