GENMOD on bigger VCF file - IO Error

[tinuthomas]

Hi,

When we tried to run GENMOD on a VCF with ~400 members in ~140 families, the code broke with this error. Why does this happen ?

Process VariantPrinter-6:
Traceback (most recent call last):
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
Process VariantAnnotator-2:
Process VariantAnnotator-5:
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py", line 160, in run
    self.run()
  File "build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py", line 160, in run
  File "build/bdist.linux-x86_64/egg/genmod/utils/variant_printer.py", line 70, in run
    self.run()
  File "build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py", line 160, in run
    variant = self.task_queue.get()
  File "<string>", line 2, in get
    self.results_queue.put(variant)
    self.results_queue.put(variant)
  File "<string>", line 2, in put
  File "<string>", line 2, in put
    self.results_queue.put(variant)
  File "<string>", line 2, in put
  File "/usr/lib64/python2.7/multiprocessing/managers.py", line 759, in _callmethod
    kind, result = conn.recv()
    kind, result = conn.recv()
    kind, result = conn.recv()
EOFError
    kind, result = conn.recv()
IOError: [Errno 104] Connection reset by peer
IOError: [Errno 104] Connection reset by peer
IOError: [Errno 104] Connection reset by peer
    self.results_queue.put(variant)
  File "<string>", line 2, in put
  File "/usr/lib64/python2.7/multiprocessing/managers.py", line 759, in _callmethod
    kind, result = conn.recv()
IOError: [Errno 104] Connection reset by peer

Also in another machine, got the error that 'no space left on the device'

Both are Linux machines. Is GENMOD creating any .tmp files/folder, if so is there a way to specify where the tmp file/folder should be generated ?

[moonso]

Ok, we never stressed test it with that many families… I can add a flag to specify where temp files should be stored if you like.

Regards,

Måns

22 apr. 2016 kl. 20:49 skrev tinuthomas notifications@github.com:

Hi,

When we tried to run GENMOD on a VCF with ~400 members in ~140 families, the code broke with this error. Why does this happen ?

Process VariantPrinter-6: Traceback (most recent call last): File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap Process VariantAnnotator-2: Process VariantAnnotator-5: Traceback (most recent call last): Traceback (most recent call last): Traceback (most recent call last): File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py", line 160, in run self.run() File "build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py", line 160, in run File "build/bdist.linux-x86_64/egg/genmod/utils/variant_printer.py", line 70, in run self.run() File "build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py", line 160, in run variant = self.task_queue.get() File "", line 2, in get self.results_queue.put(variant) self.results_queue.put(variant) File "", line 2, in put File "", line 2, in put self.results_queue.put(variant) File "", line 2, in put File "/usr/lib64/python2.7/multiprocessing/managers.py", line 759, in _callmethod kind, result = conn.recv() kind, result = conn.recv() kind, result = conn.recv() EOFError kind, result = conn.recv() IOError: [Errno 104] Connection reset by peer IOError: [Errno 104] Connection reset by peer IOError: [Errno 104] Connection reset by peer self.results_queue.put(variant) File "", line 2, in put File "/usr/lib64/python2.7/multiprocessing/managers.py", line 759, in _callmethod kind, result = conn.recv() IOError: [Errno 104] Connection reset by peer Also in another machine, got the error that 'no space left on the device'

Both are Linux machines. Is GENMOD creating any .tmp files/folder, if so is there a way to specify where the tmp file/folder should be generated ?

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[tinuthomas]

Was the temp files getting generated in the /home folder ?

Yes, please. That would be great help

[moonso]

Hi,

I have added a flag for alternative temp dirs in version 3.5.1 Please try and give feedback

Måns