Failed with exit code 1. (rc=256) #2385
Description
Hi, canu Team!
Canu process terminated unexpectedly. Can you help me?
#!/bin/bash
#SBATCH -o %x.%j.out
#SBATCH -p soy-com
#SBATCH -J canu
#SBATCH -c 90
canu -d lm_canu_assembly -p lm_canu genomeSize=1g useGrid=false maxThreads=90 -pacbio-hifi ../hifi.fq.gz
tail -n30 canu.89579.out
/hpc/home/hpc2025201067/miniforge3/envs/canu/bin/utgcns \
-S ../lm_canu.seqStore \
-T ./lm_canu.ctgStore 1 \
-partition 0.8 1.5 0.1 \
> ./lm_canu.ctgStore/partitioning.log 2>&1
-- Finished on Sat Sep 20 09:06:43 2025 (39 seconds) with 22926059.138 GB free disk space
----------------------------------------
ERROR:
ERROR: Failed with exit code 1. (rc=256)
ERROR:
ABORT:
ABORT: canu master +27 changes (r10515 2a41e933b8de6ed66723d75d36dd071b46d2c347)
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting. If that doesn't work, ask for help.
ABORT:
ABORT: failed to partition the reads.
ABORT:
ABORT: Disk space available: 22926059.138 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (unitigging/lm_canu.ctgStore/partitioning.log):
ABORT:
ABORT: -- Opening seqStore '../lm_canu.seqStore'.
ABORT: -- Using corrected-trimmed reads.
ABORT: -- Opening tigStore './lm_canu.ctgStore' version 1.
ABORT: writeBuffer()-- Failed to open file './lm_canu.ctgStore/partition.0174' with mode 'w': Too many open files
ABORT:
slurmstepd: error: common_file_write_content: unable to open '/sys/fs/cgroup/freezer/slurm/uid_1275/job_89579/step_batch/freezer.state' for writing: No such file or directory
Best!