We're running the small test data set (icAdaBipu1) on our cluster, and we're seeing some odd issues with BUSCO runs using the latest dev version.
First the solvable one. BUSCO is trying to 'call home' even when pointing to a local directory (using --offline mode), so the job just hangs. None of our worker nodes allow remote access for security reasons. We fixed this locally by modifying the section here to
withName: '.*:NUCLEAR_ASSEMBLY:GENOME_STATISTICS:BUSCO_BUSCO' {
ext.prefix = "asm"
ext.args = {
[
params.busco_lineage_directory ? "--offline --opt-out-run-stats" : "",
].join(" ").trim()
}
}
We can also do this in a local config in a pinch, but it's worth noting here in case others find the same problem.
More puzzling is the second issue. The BUSCO run completes, and we can see a valid exit in the work directory for one of the jobs:
Exit code is clean (0) and all outputs are present. But the jobs all hang:
More oddly, there are no active Nextflow jobs on the cluster queue. I suspect this is a Nextflow issue; we're using 25.10.4 so will try a newer release, but any suggestions are greatly appreciated!
We're running the small test data set (icAdaBipu1) on our cluster, and we're seeing some odd issues with BUSCO runs using the latest
devversion.First the solvable one. BUSCO is trying to 'call home' even when pointing to a local directory (using
--offlinemode), so the job just hangs. None of our worker nodes allow remote access for security reasons. We fixed this locally by modifying the section here toWe can also do this in a local config in a pinch, but it's worth noting here in case others find the same problem.
More puzzling is the second issue. The BUSCO run completes, and we can see a valid exit in the work directory for one of the jobs:
Exit code is clean (0) and all outputs are present. But the jobs all hang:
More oddly, there are no active Nextflow jobs on the cluster queue. I suspect this is a Nextflow issue; we're using 25.10.4 so will try a newer release, but any suggestions are greatly appreciated!