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aakechin / NGS-PrimerPlex

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design
GNU General Public License v3.0
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program exits with error 'The node #### is not in the graph' #21

Closed avialee closed 2 years ago

avialee commented 3 years ago

I am running NGS-PrimerPlex for a panel with ~2000 snps.

It did give some warnings that for some regions no primers left after filtering primers by specificity and that cover SNPs! There is an unreachable region '#### is not reachable from #####'.

The program failed and exits with the error shown below:

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: 48954199

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 48954199 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 3380, in poolArgs):#results: File "/usr/lib/python3.5/multiprocessing/pool.py", line 695, in next raise value networkx.exception.NetworkXError: The node 48954199 is not in the graph.

I guess it happened during 'Joining primer pairs to amplified blocks...'. Should I remove the unreachable or uncovered regions and run it again?

aakechin commented 3 years ago

@avialee Thank you for this comment! This bug is being fixed now. Sorry for this inconvenience!

aakechin commented 2 years ago

Try the new version of the NGS-PrimerPlex: https://github.com/aakechin/NGS-PrimerPlex/releases/tag/v1.3.0

Vickymj93 commented 1 year ago

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 when trying to run for a handful of SNVs (10-15). Trying to design short ampicons of size ~150bp. Any help would be appreciated.