0 edges in network 'operon' error for Halobacterium test run

[maxneal]

I recently downloaded cmonkey2 and am getting an error when I try out the Halobacterium test run. This error appears on my Ubuntu virtual machine with MEME version 4.11.2 and on a Mac (El Capitan) with MEME version 4.10.1.

Input command: bin/cmonkey2.sh --organism hal example_data/hal/halo_ratios5.tsv

Output: Running cmonkey with 'python' 2016-10-26 17:04:43 INFO checking MEME... 2016-10-26 17:04:43 INFO Input matrix has # rows: 428, # columns: 5 2016-10-26 17:04:43 INFO # clusters/row: 2 2016-10-26 17:04:43 INFO # clusters/column: 29 2016-10-26 17:04:43 INFO # CLUSTERS: 43 2016-10-26 17:04:43 INFO use operons: 1 2016-10-26 17:04:43 INFO using MEME version 4.11.2 2016-10-26 17:04:44 INFO attempting automatic download of operons from Microbes Online 2016-10-26 17:04:44 INFO NCBI CODE IS: 64091 2016-10-26 17:04:44 INFO Automatically using STRING file in 'cache/64091.gz' (URL: http://networks.systemsbiology.net/string9/64091.gz) 2016-10-26 17:04:50 INFO KEGG = 'Halobacterium NRC 1 uid57769' -> RSAT = 'Halobacterium_NRC_1_uid57769' 2016-10-26 17:04:50 INFO Creating networks... 2016-10-26 17:04:50 INFO stringdb.read_edges2() 2016-10-26 17:04:51 INFO Finished loading cache/64091.gz 2016-10-26 17:04:51 INFO Processing network 5% 2016-10-26 17:04:51 INFO Processing network 10% 2016-10-26 17:04:51 INFO Processing network 15% 2016-10-26 17:04:51 INFO Processing network 20% 2016-10-26 17:04:51 INFO Processing network 25% 2016-10-26 17:04:51 INFO Processing network 30% 2016-10-26 17:04:51 INFO Processing network 35% 2016-10-26 17:04:51 INFO Processing network 40% 2016-10-26 17:04:51 INFO Processing network 45% 2016-10-26 17:04:51 INFO Processing network 50% 2016-10-26 17:04:52 INFO Processing network 55% 2016-10-26 17:04:52 INFO Processing network 60% 2016-10-26 17:04:52 INFO Processing network 65% 2016-10-26 17:04:52 INFO Processing network 70% 2016-10-26 17:04:52 INFO Processing network 75% 2016-10-26 17:04:52 INFO Processing network 80% 2016-10-26 17:04:52 INFO Processing network 85% 2016-10-26 17:04:52 INFO Processing network 90% 2016-10-26 17:04:52 INFO Processing network 95% 2016-10-26 17:04:52 INFO Processing network 100% 2016-10-26 17:04:52 WARNING 2191 (out of 471056) nodes not found in canonical gene names 2016-10-26 17:04:52 INFO stringdb.read_edges2(), 8514 edges read, 227014 edges ignored 2016-10-26 17:04:52 INFO MicrobesOnline - make_network() 2016-10-26 17:04:52 INFO MicrobesOnline.get_operon_predictions_for(64091) 2016-10-26 17:04:52 INFO 0 prediction pairs read 2016-10-26 17:04:52 INFO 0 operons created 2016-10-26 17:04:52 INFO 0 edges computed Traceback (most recent call last): File "/home/mneal/RNAseqTools/cmonkey2/bin/cmonkey2", line 36, in cmonkey_run.run() File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/cmonkey_run.py", line 512, in run self.prepare_run() File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/cmonkey_run.py", line 474, in prepare_run thesaurus = self.organism().thesaurus() File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/cmonkey_run.py", line 231, in organism self.organism = self.make_organism() File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/cmonkey_run.py", line 341, in make_organism self['fasta_file']) File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/organism.py", line 244, in __init fasta_file) File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/organism.py", line 117, in init OrganismBase.init(self, code, network_factories, ratios=ratios) File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/organism.py", line 72, in init self.__networks.append(make_network(self, ratios)) File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/microbes_online.py", line 234, in make_network ratios, check_size) File "/home/mneal/RNAseqTools/cmonkey2/cmonkey/network.py", line 150, in create raise Exception("Error: only %d edges in network '%s'" % (len(network_edges), name)) Exception: Error: only 0 edges in network 'operons'

[weiju]

Thank you for reporting this,

it seems there has been a temporary issue with MicrobesOnline, which was fixed. Does this work for you now ?

[maxneal]

I tried the test run again just now. I still get the same error.

[weiju]

Thanks, could you please make sure that your cache directory is completely empty and retry ? Just to make sure the RSAT information got correctly read, because usually this type of error is caused by a mismatch of gene names.

BTW, MEME 4.11.x versions currently do not work with cmonkey2.

[maxneal]

After I cleared the cache it ran and completed successfully. (And BTW I had switched to meme 4.9.1 a couple weeks ago.) Thanks!

[weiju]

great to hear it works for you now, thanks !