Open Vickymj93 opened 1 year ago
Vickymj93
commented
1 year ago Although it has been working like a charm for preparing multiplex primers for amplifying regions more than 500 bp, I encountered the error mentioned above recently when running it for specifically a set of 15 defined variants in the regions file for amplification of 150bp products.
aakechin
commented
1 year ago @Vickymj93 Did you use the latest version of the NGS-PrimerPlex? 150 bp was not problem for the program. There may be other issues...
aakechin
commented
1 year ago As I see in your issue description, line numbers do not correspond to the latest version. Please, try download the latest one, and try it again. Please, give me feedback about the result.
Vickymj93
commented
1 year ago Facing the same error with a new line number when I tried to run it with the updated NGS-Primerplex1.3.4
Joining primer pairs to amplified blocks... 0.0%multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1082, in neighbors_iter return iter(self.adj[n]) KeyError: 55019216
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/lib/python3.5/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "NGS_primerplex.py", line 2192, in joinAmpliconsToBlocks path=tuple(nx.algorithms.shortest_paths.generic.shortest_path(blockGraph,firstNodes[i],lastNodes[i])) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/generic.py", line 136, in shortest_path paths=nx.bidirectional_shortest_path(G,source,target) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 136, in bidirectional_shortest_path results=_bidirectional_pred_succ(G,source,target) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 186, in _bidirectional_pred_succ for w in Gsucc(v): File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1084, in neighbors_iter raise NetworkXError("The node %s is not in the graph." % (n,)) networkx.exception.NetworkXError: The node 55019216 is not in the graph. """
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "NGS_primerplex.py", line 3795, in
petersam23
commented
1 year ago Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1082, in neighbors_iter return iter(self.adj[n]) KeyError: 20102
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/lib/python3.5/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/NGS-PrimerPlex/NGS_primerplex.py", line 2192, in joinAmpliconsToBlocks path=tuple(nx.algorithms.shortest_paths.generic.shortest_path(blockGraph,firstNodes[i],lastNodes[i])) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/generic.py", line 136, in shortest_path paths=nx.bidirectional_shortest_path(G,source,target) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 136, in bidirectional_shortest_path results=_bidirectional_pred_succ(G,source,target) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 186, in _bidirectional_pred_succ for w in Gsucc(v): File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1084, in neighbors_iter raise NetworkXError("The node %s is not in the graph." % (n,)) networkx.exception.NetworkXError: The node 20102 is not in the graph. """
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/NGS-PrimerPlex/NGS_primerplex.py", line 3795, in
Joining primer pairs to amplified blocks... 0.0%multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1082, in neighbors_iter return iter(self.adj[n]) KeyError: 55019216
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/lib/python3.5/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "NGS_primerplex.py", line 1892, in joinAmpliconsToBlocks path=tuple(nx.algorithms.shortest_paths.generic.shortest_path(blockGraph,firstNodes[i],lastNodes[i])) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/generic.py", line 136, in shortest_path paths=nx.bidirectional_shortest_path(G,source,target) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 136, in bidirectional_shortest_path results=_bidirectional_pred_succ(G,source,target) File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 186, in _bidirectional_pred_succ for w in Gsucc(v): File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1084, in neighbors_iter raise NetworkXError("The node %s is not in the graph." % (n,)) networkx.exception.NetworkXError: The node 55019216 is not in the graph. """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "NGS_primerplex.py", line 3378, in poolArgs):#results: File "/usr/lib/python3.5/multiprocessing/pool.py", line 695, in next raise value networkx.exception.NetworkXError: The node 55019216 is not in the graph.
I have been facing a similar error, to the one which user @avialee was facing, when trying to run for a handful of SNVs (10-15). Trying to design short ampicons of size ~150bp. Any help would be appreciated.