Closed chriswyatt1 closed 1 year ago
I have changed where the bind mounts of singularity are, but still cannot work out whats going on. If you have any ideas, would be great to know what I am doing wrong. Thanks. I am using singularity v3.8.5-2.el7
Here is my configuration file:
process {
executor='sge'
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.bytes/task.cpus},tmem=${task.memory.bytes/task.cpus},tscratch=${task.memory.bytes/task.cpus}" }
scratch = true
penv = { task.cpus > 1 ? 'smp' : null }
}
params {
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 36
max_time = 72.h
// igenomes_base = 's3://ngi-igenomes/igenomes/'
}
// optional executor settings
executor {
queueSize = 10
submitRateLimit = '1 sec'
}
singularity {
enabled = true
autoMounts = true
}
Sorry for not replying Chris. Saw this and then forget to respond. How did you fix it?
I'm facing the same issue. How did you solve it? Cheers!
Description of the bug
This may just be me doing something silly, but the following breaks for me on HPC, sge. Singularity is not staging the bin scritps properly I think. So the
gtf2bed
script is not found. All the other modules work as expected, its just this one that breaks the pipeline.Command used and terminal output
Relevant files
No response
System information
HPC singularity SGE. 3.9 rnaseq Version: 22.10.3 build 5834 Created: 21-11-2022 21:37 UTC (21:37 BST) System: Linux 3.10.0-1160.49.1.el7.x86_64 Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.1+12-39 Encoding: UTF-8 (UTF-8)