hyeshik
commented
5 years ago Hi @godkin1211,
The current poreplex has a problem introduced by an ABI incompatibility issue between albacore 2.3.3 and any released version of mappy. Here's a workaround:
diff --git a/poreplex/basecall_albacore.py b/poreplex/basecall_albacore.py
--- a/poreplex/basecall_albacore.py
+++ b/poreplex/basecall_albacore.py
@@ -56,6 +56,7 @@ def prepare_albacore(configpath, flowcell, kit, version_min=REQUIRED_ALBACORE_VE
config = ConfigParser(interpolation=None)
config.read_file(open(template[0]))
config['basecaller']['model_path'] = albacore_data_path
+ config['calib_detector']['method'] = ''
config.write(open(configpath, 'w'))
return __version__I am going about to release a new version which also includes the fix in a few days.
Thank you for the report!
Hi, I got an error message when running Poreplex, and it looks like poreplex did not work but just stayed in the 0% stage. The version of Albacore I used is 2.3.3 and Python version is 3.6. How do I solve this problem?
Poreplex version 0.1 by Hyeshik Chang hyeshik@snu.ac.kr
WARNING: Dashboard is turned off because it is not informative without sequence alignments.
== Analysis settings ======================================
Basecall table in output: No
==> Processing FAST5 files /home/godkin/.local/lib/python3.6/site-packages/poreplex/basecall_albacore.py:83: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. for field in field_names]) /home/godkin/.local/lib/python3.6/site-packages/poreplex/basecall_albacore.py:83: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. for field in field_names]) /home/godkin/.local/lib/python3.6/site-packages/poreplex/basecall_albacore.py:83: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. for field in field_names]) /home/godkin/.local/lib/python3.6/site-packages/poreplex/basecall_albacore.py:83: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. for field in field_names]) Exception in thread Thread-1: | Elapsed: 0:00:03 ETA: --:--:-- Traceback (most recent call last): File "/usr/lib/python3.6/threading.py", line 916, in _bootstrap_inner self.run() File "/usr/lib/python3.6/threading.py", line 864, in run self._target(*self._args, **self._kwargs) File "/usr/lib/python3.6/concurrent/futures/process.py", line 295, in _queue_management_worker shutdown_worker() File "/usr/lib/python3.6/concurrent/futures/process.py", line 253, in shutdown_worker call_queue.put_nowait(None) File "/usr/lib/python3.6/multiprocessing/queues.py", line 129, in put_nowait return self.put(obj, False) File "/usr/lib/python3.6/multiprocessing/queues.py", line 83, in put raise Full queue.Full
Exception ignored when trying to write to the signal wakeup fd: BlockingIOError: [Errno 11] Resource temporarily unavailable Exception ignored when trying to write to the signal wakeup fd: BlockingIOError: [Errno 11] Resource temporarily unavailable Exception ignored when trying to write to the signal wakeup fd: | Elapsed: 0:00:04 ETA: --:--:-- BlockingIOError: [Errno 11] Resource temporarily unavailable 0% of 71315 | | Elapsed: 0:03:17 ETA: --:-