General Troubleshooting


Error: Failed to allocate memory

If f5c exited with a “Failed to allocate memory” error, it means that the free RAM available on the system was not adequate. The peak RAM usage in f5c can be reduced by lowering the batch size parameters (-K and B). Reducing the number of threads (-t) also helps to reduce the peak RAM usage.

Another factor that affects the RAM usage is the abundance of ultra-long reads. This is particularly the case if the error occurred in align.c. Peak RAM usage due to ultra-long reads can be reduced by skipping the ultra-long reads (–skip-ultra tmp.bam). If f5c still exits with the same error, you can reduce the threshold for ultra-long reads (e.g., –skip-ultra tmp.bam –ultra-thresh 50000).

f5c crashes / get killed / segmentation fault

Linux allows memory overcommitment, i.e., programs are allowed to allocate more than the physical RAM available on the system, with the assumption that not all programmes will use the allocated memory at once. However, when the system is running low on physical memory, the Out Of Memory (OOM) killer in Linux kills memory-hogging programmes. If f5c abruptly crashed (sometimes with the message “killed”, but may also be a “segmentation fault”), it is likely to be due to high peak memory. You can verify this if you run the dmesg command on the terminal and observe a message like “Out of memory: Kill process X or sacrifice child”. Use the same techniques discussed above (Error: Failed to allocate memory topic) to reduce the peak memory usage of f5c.

The fast5 file is compressed with VBZ but the required plugin is not loaded

This is due to the vbz compression used in the latest fast5 files. You need to setup the vbz plugin for HDF5. We have provided a helper script in f5c which you can invoke as scripts/ This script attempts to determine your operating system and the arcihtecture, downloads and extract the plugin (.so file) to $HOME/.local/hdf5/lib/plugin. You must export the path to the plugin by invoking export HDF5_PLUGIN_PATH=$HOME/.local/hdf5/lib/plugin . Note that the exported environmental variable will not persist accross different shells. For persistence, you must add export HDF5_PLUGIN_PATH=$HOME/.local/hdf5/lib/plugin to your ~/.bashrc or /etc/environment.

Our helper script currently supports Linux on x86_64 and aarch64 architectures only. If your system is of a different operating system and/or architecture (or if this helper script fails) you have to download and manually install the plugin from here. See this post for troubleshooting a manual installation.