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Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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''Node not found'' issue #36

Closed Ksalanin closed 5 years ago

Ksalanin commented 5 years ago

Hi

Im trying to use recycler for identifying circular elements from a mobilome (extracted plasmids from an environmental sample)

when i run the command: recycle.py -g ../assembly_graph.fastg -k 127 -b reads_pe_primary.sort.bam -i False -o .

I get the error back after a little time:

Traceback (most recent call last): File "/usr/local/bin/recycle.py", line 4, in import('pkg_resources').run_script('recycler==0.62', 'recycle.py') File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 1445, in run_script exec(script_code, namespace, namespace) File "/usr/local/lib/python2.7/dist-packages/recycler-0.62-py2.7.egg/EGG-INFO/scripts/recycle.py", line 173, in

File "build/bdist.linux-x86_64/egg/recyclelib/utils.py", line 340, in is_good_cyc File "build/bdist.linux-x86_64/egg/recyclelib/utils.py", line 324, in get_contigs_of_mates File "/usr/local/lib/python2.7/dist-packages/networkx/algorithms/shortest_paths/generic.py", line 40, in has_path nx.shortest_path(G, source, target) File "/usr/local/lib/python2.7/dist-packages/networkx/algorithms/shortest_paths/generic.py", line 170, in shortest_path paths = nx.bidirectional_shortest_path(G, source, target) File "/usr/local/lib/python2.7/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 223, in bidirectional_shortest_path raise nx.NodeNotFound(msg.format(source, target)) networkx.exception.NodeNotFound: Either source EDGE_10343701_length_848_cov_11.642164' or target EDGE_10682581_length_5431_cov_2.680430 is not in G

Thanks in advance for your help :)

dpellow commented 5 years ago

Thanks for the report, I believe the latest bug fix solved this issue. Please let us know if it has fixed the problem on your input files.