Troubleshooting

Troubleshooting

The application does not start on Linux

Run the launcher from a terminal:

cd insilicoPCR-linux-x64
chmod +x run-insilicoPCR.sh
./run-insilicoPCR.sh

Check the terminal output for missing files or permission errors.

Permission denied on Linux

Make the launcher executable:

chmod +x run-insilicoPCR.sh

If needed, also ensure bundled tool scripts are executable.

The application does not start on Windows

Make sure the ZIP was fully extracted before running the launcher.

Run:

run-insilicoPCR.bat

Do not run the application directly from inside the ZIP archive.

Windows SmartScreen warning

Windows may warn about unsigned software.

Only continue if the release was downloaded from the official repository.

Missing Java

Portable releases include a bundled Java runtime. You should not need system Java.

If Java is reported missing, the release folder may be incomplete or files may have been moved after extraction.

Missing BBMap or BLAST+

Portable releases include BBMap and BLAST+.

If a tool is reported missing:

• confirm the ZIP was fully extracted
• keep the runtime/ folder beside the launcher
• do not move files out of the release folder

Primer file errors

Primer FASTA IDs must end with:

• -F
• -R
• -P for probes

See Primer FASTA Format.

Missing positive results in mixed primer files

Do not mix standard PCR assays and qPCR/probe assays in the same primer FASTA file.

If any assay includes a -P probe, the consolidated report runs in qPCR mode and assays without probes may not be reported as positive.

CLI help

Use:

./runtime/linux/jdk/bin/java -jar insilicoPCR.jar -h