spades assembly sample

Question

[MEITUO]

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.

[JC]

I guess you are running this on a server/cluster with a shared directory, the error OSError: [Errno 116] Stale file handle could occur because the filesystem was not fast enough to sync the file status as in NFS. You can try to rerun this to see if that happens again.

[MEITUO]

hi!

thanks for your answer.

i had rerun this, but still same error