Hi everyone!

I am using spades to assembly my sample. the command line:

spades.py --meta -1 qc_reads/DP_Sample016_S16_adapter_phix_moving_sickle_R1_sss.fastq.gz -2 qc_reads/DP_Sample016_S16_adapter_phix_moving_sickle_R2_sss.fastq.gz -m 500 -t 35 -k 21,33,55 -o assembly_plasmidome/DP_Sample016_S16_spades_res

The error is:

--- Logging error ---
Traceback (most recent call last):
  File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/f78fb5b7/lib/python3.9/logging/__init__.py", line 1083, in emit
    self.flush()
  File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/f78fb5b7/lib/python3.9/logging/__init__.py", line 1063, in flush
    self.stream.flush()
OSError: [Errno 116] Stale file handle
Call stack:
  File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/f78fb5b7/bin/spades.py", line 639, in <module>
    main(sys.argv)
  File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/f78fb5b7/bin/spades.py", line 606, in main
    executor.execute(commands)
  File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/f78fb5b7/share/spades/spades_pipeline/executors/executor_local.py", li
ne 37, in execute
    command.run(self.log)
  File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/f78fb5b7/share/spades/spades_pipeline/commands_parser.py", line 38, in
 run
    support.sys_call(self.to_list(), log)
  File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/f78fb5b7/share/spades/spades_pipeline/support.py", line 260, in sys_ca
ll
    log.info(line)
Message: '  0:07:25.844     2G / 2G    INFO   K-mer Counting           (kmer_data.cpp             : 321)   Processed 5202793 reads'
Arguments: ()

Does anybody know what happened? And I have few samples, but only this one has this problem.