The RDP Classifier (written in Java) runs out of memory when running it on the memory-controlled Rosalind HPC. So, RDP dir and outfiles aren't generated in v2.3.0 of the workflow.
cd .work/
find . -name "*RDP*" -print
cd `dirname ./34/d572036fe80c54c17eac77332976d8/ETB229_S257_L001.RDP.tsv`
% cat .command.out
[2024-Apr-29 Mon 17:51:12] INFO: Performing RDP 16S Classification
[2.040s][warning][os,thread] Failed to start thread "G1 Refine#11" - pthread_create failed (EAGAIN) for attributes: stacksize: 1024k, guardsize: 4k, detached.
[2.041s][warning][gc ] Failed to create refinement thread 11, no more OS threads
[thread 219 also had an error][thread 216 also had an error][thread 218 also had an error][thread 158 also had an error]
[thread 214 also had an error]
[thread 159 also had an error]
[thread 156 also had an error]
[thread 157 also had an error]
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (malloc) failed to allocate 64 bytes for AllocateHeap
# An error report file with more information is saved as:
# .work/34/d572036fe80c54c17eac77332976d8/hs_err_pid46.log
Description of the bug
The RDP Classifier (written in Java) runs out of memory when running it on the memory-controlled Rosalind HPC. So, RDP dir and outfiles aren't generated in v2.3.0 of the workflow.
% cat .command.outCommand used and terminal output
No response
Relevant files
No response
System information
Rosalind HPC issue ; local run is fine