Core dump when processing example

[tillea]

Hi,
I tested falco with an example fastq file I've found in the FastQC source:

$ falco example.fastq
[limits]        using file ./Configuration/limits.txt
[adapters]      using file ./Configuration/adapter_list.txt
[contaminants]  using file ./Configuration/contaminant_list.txt
[Tue Jun  9 21:18:09 2026] Started reading file example.fastq
[Tue Jun  9 21:18:09 2026] reading file as uncompressed FASTQ format
Segmentation fault         (core dumped) falco example.fastq

Kind regards, Andreas.

example.fastq.zip

[andrewdavidsmith]

@tillea Can I get more info? I only see these two files in the source repo from FastQC just updated now:

./test/data/complex.fastq
./test/data/minimal.fastq

Neither segfaulted, but I would still need to know which version of falco you're using.

[tillea]

I've attached the example file. Just unzip it.

I used the data from the autopkgtest of the Debian fastqc package

[andrewdavidsmith]

@tillea Thanks. Got it and I can reproduce the problem.

[andrewdavidsmith]

@tillea That file had an extra (empty) line at the end. I updated falco to detect this and consider it an error which is in release v1.3.2 (PR #98). Thanks very much for pointing out the issue.

I encourage you to look at https://github.com/andrewdavidsmith/falco2/ which will be merged into this repo. Though still in progress, it is fully accurate for almost all outputs, and has significantly improved performance on most kinds of inputs and most hardware.

[tillea]

Thanks a lot for the quick response which fixed the core dump. However, now the processing ends in

encountered invalid read number: 126

which is also a difference to FastQC. If you think falco2 will feature reproducible results with FastQC I can wait with the Debian packaging until this is merged.