Error IOError: [Errno 13] Permission denied:

[pedrogribeiro]

Hi, all!

This is my first time running SPAdes and I am running it with PBS on a cluster and getting the following message as error:

== Error ==  system call for: "['/afs/ics.muni.cz/software/spades/3.9.0/bin/hammer', '/storage/brno3-cerit/home/pedroribeiro/eudaminae_analyses/out_spades_test/corrected/configs/config.info']" finished abnormally, err code: -6
[Errno 13] Permission denied: '/storage/brno3-cerit/home/pedroribeiro/eudaminae_analyses/out_spades_test/spades.log'
Traceback (most recent call last):
  File "/software/spades/3.9.0/bin/spades.py", line 694, in main
    ext_python_modules_home, only_compressing_is_needed, log)
  File "/afs/ics.muni.cz/software/spades/3.9.0/share/spades/spades_pipeline/hammer_logic.py", line 138, in run_hammer
    support.sys_call(command, log)
  File "/afs/ics.muni.cz/software/spades/3.9.0/share/spades/spades_pipeline/support.py", line 218, in sys_call
    error('system call for: "%s" finished abnormally, err code: %d' % (cmd, proc.returncode), log)
  File "/afs/ics.muni.cz/software/spades/3.9.0/share/spades/spades_pipeline/support.py", line 41, in error
    log_warnings(log, with_error=True)
  File "/afs/ics.muni.cz/software/spades/3.9.0/share/spades/spades_pipeline/support.py", line 347, in log_warnings
    spades_py_warns, spades_warns = get_important_messages_from_log(log_file, warnings=True)
  File "/afs/ics.muni.cz/software/spades/3.9.0/share/spades/spades_pipeline/support.py", line 312, in get_important_messages_from_log
    lines_to_check = open(log_filename, 'r').readlines()
IOError: [Errno 13] Permission denied: '/storage/brno3-cerit/home/pedroribeiro/eudaminae_analyses/out_spades_test/spades.log'

== Error ==  exception caught: <type 'exceptions.IOError'>

So I am not quite sure if it is only a memory issue because of the err code: -6 or if it is the Errno 13 Permission denied which is causing it to Exit the job.

Any help would appreciated and don't exactly what other information to add but will be happy to give it if needed!

Thanks a lot!

[asl]

So, the log clearly reads:

[Errno 13] Permission denied: '/storage/brno3-cerit/home/pedroribeiro/eudaminae_analyses/out_spades_test/spades.log'

It seems you do not have some necessary write permissions or there is an I/O error on your storage. I would suggest you to contact your system administrator.

PS: SPAdes 3.9 is really ancient. Consider upgrading

[pedrogribeiro]

Great! Thanks a lot, appreciate it!