recursive_search_clusters errors when running denovo kappa
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#1 recursive_search_clusters errors when running denovo kappa
Hello
I've been trying to run kappa to find new patters of disulfide rich proteins in my dataset.
Here is a snippet of the error out file:
Traceback (most recent call last):
File "/opt/Modules//kappa/1.0//bin/kappa", line 4024, in <module>
clusters, sequence_edges, node_attributes, report = make_clusters(mapping_scores, threads, score_thr_pass1, score_thr_pass2, fusion_thr, report, optimization)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1434, in make_clusters
global_network, local_network = recursive_search_clusters(node, sequence_edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)</module>
It seems to run fine otherwise but what is causing this error that eventually leads to a runtime error:
...
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1393, in recursive_search_clusters
if neighbor_node not in local_network:
RuntimeError: maximum recursion depth exceeded in comparison
Any insight into what problem I might be having would be great.
Cheers
Ed
Hello,
I am sorry to hear that you are experiencing problems with KAPPA. The issue seems to be related to recursion depth: due to a large number of sequences and/or permissive clustering criteria, a large cluster is formed and it is big enough for the recursive clustering function to meet the maximum recursion depth allowed on your system.
I have just uploaded a new kappa-1.1 version with minor adjustment, including a higher maximum recursion depth. If it is still not enough for your sequences, you may want to manually edit line 40 in the bin/kappa file:
to set the recursion limit to a higher value.
I hope this helped you!
Cheers,
Valentin
Hello Valentin
Thank you very much for your quick response. It is very much appreciated. We are attempting to use the new version soon and I'll let you know how it goes.
Best wishes
Ed
Dr. Edward K Gilding | Postdoctoral Researcher
Institute for Molecular Bioscience
Level 2 North | 306 Carmody Road (Building 80) | The University of Queensland | Brisbane QLD 4072 Australia
T +61 7 3346 2014 | F +61 7 3346 2101 | E e.gilding@imb.uq.edu.au
imb.uq.edu.auhttp://www.imb.uq.edu.au | Facebookhttp://www.facebook.com/instituteformolecularbioscience | Twitterhttp://www.twitter.com/IMBatUQ | YouTubehttp://www.youtube.com/IMBatUQ
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From: Valentin Joly [mailto:valentinjoly@users.sf.net]
Sent: Friday, 17 March 2017 1:52 AM
To: [kappa-sequence-search:tickets]
Subject: [kappa-sequence-search:tickets] #1 recursive_search_clusters errors when running denovo kappa
Hello,
I am sorry to hear that you are experiencing problems with KAPPA. The issue seems to be related to recursion depth: due to a large number of sequences and/or permissive clustering criteria, a large cluster is formed and it is big enough for the recursive clustering function to meet the maximum recursion depth allowed on your system.
I have just uploaded a new kappa-1.1 version with minor adjustment, including a higher maximum recursion depth. If it is still not enough for your sequences, you may want to manually edit line 40 in the bin/kappa file:
sys.setrecursionlimit(20000)
to set the recursion limit to a higher value.
I hope this helped you!
Cheers,
Valentin
[tickets:#1]https://sourceforge.net/p/kappa-sequence-search/tickets/1/ recursive_search_clusters errors when running denovo kappa
Status: open
Milestone: 1.0
Created: Thu Mar 16, 2017 05:08 AM UTC by Edward Gilding
Last Updated: Thu Mar 16, 2017 05:08 AM UTC
Owner: nobody
Hello
I've been trying to run kappa to find new patters of disulfide rich proteins in my dataset.
Here is a snippet of the error out file:
Traceback (most recent call last):
File "/opt/Modules//kappa/1.0//bin/kappa", line 4024, in <module>
clusters, sequence_edges, node_attributes, report = make_clusters(mapping_scores, threads, score_thr_pass1, score_thr_pass2, fusion_thr, report, optimization)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1434, in make_clusters
global_network, local_network = recursive_search_clusters(node, sequence_edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)</module>
It seems to run fine otherwise but what is causing this error that eventually leads to a runtime error:
...
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1393, in recursive_search_clusters
if neighbor_node not in local_network:
RuntimeError: maximum recursion depth exceeded in comparison
Any insight into what problem I might be having would be great.
Cheers
Ed
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Hello Valentin
The v1.1 update works great! Thank you for the quick response again.
Best wishes
Ed
Dr. Edward K Gilding | Postdoctoral Researcher
Institute for Molecular Bioscience
Level 2 North | 306 Carmody Road (Building 80) | The University of Queensland | Brisbane QLD 4072 Australia
T +61 7 3346 2014 | F +61 7 3346 2101 | E e.gilding@imb.uq.edu.au
imb.uq.edu.auhttp://www.imb.uq.edu.au | Facebookhttp://www.facebook.com/instituteformolecularbioscience | Twitterhttp://www.twitter.com/IMBatUQ | YouTubehttp://www.youtube.com/IMBatUQ
[signature]http://www.imb.uq.edu.au/
This email (including any attached files) is intended solely for the addressee. It may contain private or confidential information. If you are not the intended addressee, you must take no action based on it, nor show a copy to anyone. Kindly notify the sender by reply email. Opinions and information in this email which do not relate to the official business of The University of Queensland shall be understood as neither given nor endorsed by the University. CRICOS Provider Number 00025B.
From: Valentin Joly [mailto:valentinjoly@users.sf.net]
Sent: Friday, 17 March 2017 1:52 AM
To: [kappa-sequence-search:tickets]
Subject: [kappa-sequence-search:tickets] #1 recursive_search_clusters errors when running denovo kappa
Hello,
I am sorry to hear that you are experiencing problems with KAPPA. The issue seems to be related to recursion depth: due to a large number of sequences and/or permissive clustering criteria, a large cluster is formed and it is big enough for the recursive clustering function to meet the maximum recursion depth allowed on your system.
I have just uploaded a new kappa-1.1 version with minor adjustment, including a higher maximum recursion depth. If it is still not enough for your sequences, you may want to manually edit line 40 in the bin/kappa file:
sys.setrecursionlimit(20000)
to set the recursion limit to a higher value.
I hope this helped you!
Cheers,
Valentin
[tickets:#1]https://sourceforge.net/p/kappa-sequence-search/tickets/1/ recursive_search_clusters errors when running denovo kappa
Status: open
Milestone: 1.0
Created: Thu Mar 16, 2017 05:08 AM UTC by Edward Gilding
Last Updated: Thu Mar 16, 2017 05:08 AM UTC
Owner: nobody
Hello
I've been trying to run kappa to find new patters of disulfide rich proteins in my dataset.
Here is a snippet of the error out file:
Traceback (most recent call last):
File "/opt/Modules//kappa/1.0//bin/kappa", line 4024, in <module>
clusters, sequence_edges, node_attributes, report = make_clusters(mapping_scores, threads, score_thr_pass1, score_thr_pass2, fusion_thr, report, optimization)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1434, in make_clusters
global_network, local_network = recursive_search_clusters(node, sequence_edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)</module>
It seems to run fine otherwise but what is causing this error that eventually leads to a runtime error:
...
File "/opt/Modules//kappa/1.0//bin/kappa", line 1394, in recursive_search_clusters
global_network, local_network = recursive_search_clusters(neighbor_node, edges, global_network, local_network)
File "/opt/Modules//kappa/1.0//bin/kappa", line 1393, in recursive_search_clusters
if neighbor_node not in local_network:
RuntimeError: maximum recursion depth exceeded in comparison
Any insight into what problem I might be having would be great.
Cheers
Ed
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Hi Edward,
You’re very welcome! Please do not hesitate to contact me should you need help again.
Regards,
Valentin