levinas / assembly Goto Github PK

ERROR:pika.adapters.base_connection:Socket Error on fd 12: 104
WARNING:pika.adapters.base_connection:Socket closed when connection was open
Process [Worker 5]::
Traceback (most recent call last):
  File "/vol/kbase/runtime/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/vol/kbase/runtime/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/disks/arast/fangfang/assembly/lib/assembly/consume.py", line 376, in start
    self.fetch_job()
  File "/disks/arast/fangfang/assembly/lib/assembly/consume.py", line 350, in fetch_job
    channel.start_consuming()
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 955, in start_consuming
    self.connection.process_data_events()
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 240, in process_data_events
    if self._handle_read():
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 348, in _handle_read
    super(BlockingConnection, self)._handle_read()
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/base_connection.py", line 351, in _handle_read
    self._on_data_available(data)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/connection.py", line 1285, in _on_data_available
    self._process_frame(frame_value)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/connection.py", line 1365, in _process_frame
    self._deliver_frame_to_channel(frame_value)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/connection.py", line 976, in _deliver_frame_to_channel
    return self._channels[value.channel_number]._handle_content_frame(value)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/channel.py", line 792, in _handle_content_frame
    self._on_deliver(*response)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/channel.py", line 886, in _on_deliver
    body)
  File "/disks/arast/fangfang/assembly/lib/assembly/consume.py", line 372, in callback
    ch.basic_ack(delivery_tag=method.delivery_tag)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/channel.py", line 147, in basic_ack
    return self._send_method(spec.Basic.Ack(delivery_tag, multiple))
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 1159, in _send_method
    self.connection.send_method(self.channel_number, method_frame, content)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 274, in send_method
    self._send_method(channel_number, method_frame, content)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/connection.py", line 1503, in _send_method
    self._send_frame(frame.Method(channel_number, method_frame))
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 417, in _send_frame
    super(BlockingConnection, self)._send_frame(frame_value)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/connection.py", line 1490, in _send_frame
    self._flush_outbound()
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 377, in _flush_outbound
    if self._handle_write():
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/base_connection.py", line 365, in _handle_write
    return self._handle_error(error)
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/base_connection.py", line 302, in _handle_error
    self._handle_disconnect()
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/base_connection.py", line 248, in _handle_disconnect
    self._adapter_disconnect()
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 318, in _adapter_disconnect
    self._check_state_on_disconnect()
  File "/vol/kbase/runtime/lib/python2.7/site-packages/pika/adapters/blocking_connection.py", line 371, in _check_state_on_disconnect
    raise exceptions.ConnectionClosed()
ConnectionClosed

|  340   |   210   |            Stage 1/9: bhammer            | 0:02:26  |   b12.smart    |
|  341   |   210   |            Stage 2/4: spades             | 0:02:26  |    b12.fast    |
|  342   |   210   |            Stage 1/7: bhammer            | 0:00:30  |    b12.auto    |
|  343   |   210   |            Stage 1/4: velvet             | 0:00:00  |   b12.miseq    |

@M00963:74:000000000-A3DM3:1:1101:15651:1404 1:N:0:7
GNCAGAAACAGGCCCACGAGATAGAAAACGCGCGCAATGCGGCGGCGCATACGGTGTTGGGCATTGCTCAAGGATTGGGCCATGACTACCACTCCGCTCCGATCTGCGTGCGCGCGGCGGCAAGCTTGCGGAAGAAAATGACGGTGAAGAGGATGGAGAGAAGGATCGCGACATAGGCCATGGCATTGGCAAGGCCCATCTGCGCATCCGAGTAGGCCGTGCGGCCCACGAGGGTCCAGATCAGCTCCGTG
+
A#>>AAAFFBCAF1EGGGGCGCFHGHHFHC?EGGCGGGFHCCG?EECGGGGHFGHHGGG/CAHHHHHFHGHHGHHHGGGHHGHGFHGHHHHFHHHGGGGGC@FGHHHCEFFCCCGG?AG?@;9EFFFF?@@?@BFFFFFFFFF@BAEBFFAEFFF?FFFFFFFFFFF??-@@@FFEFFFFFFFEFFFFEFBFEEE-BFFFFFE@@@F<FFF@9A9/BF?@?B@@;@@BF@-9>-BF-BFFFFFF/;F/AEE
@M00963:74:000000000-A3DM3:1:1101:16929:1411 1:N:0:7
GTTCCGACATCGACCTTCTTTTCCTGCTTCCCTATAAACAGACGCCCTGGGGCGAACAGGTTGTGGAATATACGCTCTACATGCTCTGGGACATGGGGCTGAAAGTCGGCCATTCCACCCGCAACATCGATGAGTGCATTCGTCTGGCGCGCGAGGACATGACCATTCGCACAGCCCTTCTCGATGCGCGCTTTCTTACCGGCGACAAGGATCTGTTCCGCACACTTGAAATCCGTTTCGAGGAGGAAAT
+
3A?3AAABBBFBFGGGGGGGGGFFFGGHHHHHHHHHHHHHHHHGEEGGHFEGGGGGGGHGHHHEEGGHHHHHHGGGGGGHHHGHGFGHHHHHGHFFHGGCDCHFH?GABGGGHGBGGGAGGCFGGGFHGGHHFHHHFHEFHHHGHGHG@ADGGGGCCGGGBBFGFGBBFGGGGFGFCFFFEFFBFF?>DDACFFBBBFFFFFFA>DFFFFFFFF/BFFF?DF;;.BFFFFF//9A9FB/AEF;;AD.FBF