allista/degenprimer

DegenPrimer is a tool to check the quality of degenerate primers by simulating PCR

degenprimer's Issues

ImportError: No module named StringTools

Traceback (most recent call last):
  File "./DegenPrimer/degen_primer", line 25, in <module>
    from DegenPrimer.StringTools import hr, wrap_text
ImportError: No module named StringTools

Broken pipe

I am running a conda env containing DegenPrimer and its required dependencies. I receive an error regarding a broken pipe when running this with a degenerate primer set on 300 + norovirus sequences. The cfg file is attached (and reformatted as a txt file for the purpose of logging an issue).

[2023-06-21 16:52:59,143] [2] [ 62.50%] [21.06.2023 16:52:59] PCR Simulation: calculating equilibrium in the system and running the simulation... [2023-06-21 16:53:05,218] [1] [ 68.24%] [21.06.2023 16:53:05] elapsed: 0:02:31.709365 [2023-06-21 16:53:06,191] [Errno 32] Broken pipe [2023-06-21 16:53:06,206] Exception occured: Traceback (most recent call last): File "DegenPrimer/DegenPrimer/AnalysisTask.py", line 300, in run self._listen_subroutines() File "DegenPrimer/DegenPrimer/AnalysisTask.py", line 263, in _listen_subroutines else: self._print_counters() File "DegenPrimer/DegenPrimer/AnalysisTask.py", line 227, in _print_counters if p_entry.counter.last_checked() < self._counter_threshold: continue File "<string>", line 2, in last_checked File "conda/degenprimer_env/lib/python2.7/multiprocessing/managers.py", line 758, in _callmethod conn.send((self._id, methodname, args, kwds)) IOError: [Errno 32] Broken pipe [2023-06-21 16:53:09,189] Error in thread: Calculate relative concentrations of secondary structures at Tm. [2023-06-21 16:53:09,201] Traceback (most recent call last): File "conda/degenprimer_env/lib/python2.7/site-packages/BioUtils/Tools/Debug.py", line 67, in wrapper try: return func(*args, **kwargs) File "DegenPrimer/DegenPrimer/AllSecStructures.py", line 142, in calculate_equilibrium counter[2].count() File "<string>", line 2, in __getitem__ File "conda/degenprimer_env/lib/python2.7/multiprocessing/managers.py", line 771, in _callmethod conn = self._Client(token.address, authkey=self._authkey) File "conda/degenprimer_env/lib/python2.7/multiprocessing/connection.py", line 169, in Client c = SocketClient(address) File "conda/degenprimer_env/lib/python2.7/multiprocessing/connection.py", line 308, in SocketClient s.connect(address) File "conda/degenprimer_env/lib/python2.7/socket.py", line 228, in meth return getattr(self._sock,name)(*args) error: [Errno 2] No such file or directory [2023-06-21 16:53:55,354] === END LOGGING ===
MON431-G2SKR_109377931.txt

Alternatively if I comment out line 227 in AnalysisTask.py I can get a bit further:

[2023-06-21 16:53:06,206] Exception occured:
Traceback (most recent call last):
  File "DegenPrimer/DegenPrimer/AnalysisTask.py", line 300, in run
    self._listen_subroutines()
  File "DegenPrimer/DegenPrimer/AnalysisTask.py", line 263, in _listen_subroutines
    else: self._print_counters()
  File "DegenPrimer/DegenPrimer/AnalysisTask.py", line 227, in _print_counters
    if p_entry.counter.last_checked() < self._counter_threshold: continue
  File "<string>", line 2, in last_checked
  File "conda/degenprimer_env/lib/python2.7/multiprocessing/managers.py", line 758, in _callmethod
    conn.send((self._id, methodname, args, kwds))
IOError: [Errno 32] Broken pipe
[2023-06-21 16:53:09,189] Error in thread: Calculate relative concentrations of secondary structures at Tm.
[2023-06-21 16:53:09,201] Traceback (most recent call last): File "conda/degenprimer_env/lib/python2.7/site-packages/BioUtils/Tools/Debug.py", line 67, in wrapper try: return func(*args, **kwargs) File "DegenPrimer/DegenPrimer/AllSecStructures.py", line 142, in calculate_equilibrium counter[2].count() File "<string>", line 2, in __getitem__ File "conda/degenprimer_env/lib/python2.7/multiprocessing/managers.py", line 771, in _callmethod conn = self._Client(token.address, authkey=self._authkey) File "conda/degenprimer_env/lib/python2.7/multiprocessing/connection.py", line 169, in Client c = SocketClient(address) File "conda/degenprimer_env/lib/python2.7/multiprocessing/connection.py", line 308, in SocketClient s.connect(address) File "conda/degenprimer_env/lib/python2.7/socket.py", line 228, in meth return getattr(self._sock,name)(*args) error: [Errno 2] No such file or directory
[2023-06-21 16:53:55,354] === END LOGGING ===