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Semibin error exit status 137

#996Closedbioinfo-arctic 创建于 2026-03-11
bug
B
bioinfo-arcticcommented
### Description of the bug I am seeing repeated failures in: NFCORE_MAG:MAG:BINNING:SEMIBIN_SINGLEEASYBIN with exit status 137. The task stderr shows only "Killed", and dmesg confirms it is being OOM-killed inside the Docker memory cgroup. Examples from dmesg: Memory cgroup out of memory: Killed process 1739457 (SemiBin2) total-vm:472319276kB, anon-rss:36381296kB, file-rss:113872kB, shmem-rss:0kB, UID:1007 pgtables:145912kB oom_score_adj:0 Memory cgroup out of memory: Killed process 3556228 (SemiBin2) total-vm:477333324kB, anon-rss:104084912kB, file-rss:112924kB, shmem-rss:0kB, UID:1007 pgtables:304708kB oom_score_adj:0 Memory cgroup out of memory: Killed process 2722988 (SemiBin2) total-vm:473160272kB, anon-rss:364931412kB, file-rss:113376kB, shmem-rss:0kB, UID:1007 pgtables:812484kB oom_score_adj:0 I set: withName: 'NFCORE_MAG:MAG:BINNING:SEMIBIN_SINGLEEASYBIN' { cpus = 8 memory = 360.GB time = 96.h } but inspecting .command.run shows the container was actually launched with: --memory 147456m <img width="2307" height="68" alt="Image" src="https://github.com/user-attachments/assets/fda7df2e-c970-4764-a424-abf0c6ee5583" /> which is ~144 GB, not 360 GB. So it looks like the process-specific memory request is being capped somewhere before Docker launch. ### Command used and terminal output ```console ``` ### Relevant files _No response_ ### System information _No response_
关闭于 2026-03-30 2 条评论