Reported by @ashildv and replicated by me.
FastQC has a hard memory usage limit of 250MB, which can only be increased by adding more threads (with -t). As fastqc is written in java, it seems it doesn't 'die' when it gets a GC overhead limit error, and just keeps running forever
Exception in thread "Thread-1" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.Arrays.copyOfRange(Arrays.java:3664)
at java.lang.String.<init>(String.java:207)
at java.io.BufferedReader.readLine(BufferedReader.java:356)
at java.io.BufferedReader.readLine(BufferedReader.java:389)
I tested manually on the errored files by increasing threads to 2 and this then worked correctly.
Therefore the solution would be to switch fastqc from sc_small to mc_small.
Reported by @ashildv and replicated by me.
FastQC has a hard memory usage limit of 250MB, which can only be increased by adding more threads (with
-t). As fastqc is written in java, it seems it doesn't 'die' when it gets a GC overhead limit error, and just keeps running foreverI tested manually on the errored files by increasing threads to 2 and this then worked correctly.
Therefore the solution would be to switch fastqc from
sc_smalltomc_small.