Failures during the run¶
no usable clip range¶
CLIPPING READS <sample>: ERROR: no usable clip range in <file>
CLIPPING READS <sample>: exit 3 = unexpected FastQC header; 4 = no cycle within at_gc_error (0.025)
Exit 4 means no read cycle had A/T and G/C ratios inside at_gc_error. On a GC-skewed genome this is expected, not a fault. Raise at_gc_error.
Exit 3 means the FastQC per-base composition table did not have the expected A/T/G/C columns, which points at a FastQC version change or a corrupt report.
Symbolic link errors¶
Confirm you are on Linux. macOS and Windows (including WSL under some filesystem configurations) are not supported. Also check that storageDir is still mounted and was not cleared while the run was in flight.
A step fails and I cannot tell why¶
.nextflow.log names the failing process. Each step also mirrors its own .command.log and .command.err into Logs/<step>/, which is usually more readable.
For a reproducible failure, set threads = 1. That removes concurrency as a variable and makes the logs sequential.