[BUG] ValueError occurred after running anvi-reaction-network

yqy6611 commented 11 months ago

Short description of the problem

"ValueError: max() arg is an empty sequence" was encountered after running anvi-reaction-network.

anvi'o version

Anvi'o .......................................: marie (v8-dev) Python .......................................: 3.10.13

Profile database .............................: 39 Contigs database .............................: 22 Pan database .................................: 17 Genome data storage ..........................: 7 Auxiliary data storage .......................: 2 Structure database ...........................: 2 Metabolic modules database ...................: 4 tRNA-seq database ............................: 2

System info

Ubuntu 22.04; following https://anvio.org/install/linux/dev/.

Detailed description of the issue

"ValueError: max() arg is an empty sequence" was encountered after running anvi-reaction-network. Attached is the verbose:

(anvio-dev) e2s2@e2s2-super-server-1:/mnt/b351004a-4dc6-4bcf-add3-21fc26707773/Eric_meta$ anvi-reaction-network -c '/mnt/b351004a-4dc6-4bcf-add3-21fc26707773/Eric_meta/GB_GCA_001567165_1.db' --ko-dir '/mnt/cc061462-beb3-49ab-9318-5c7bf54d8588/database/anvio-KEGG/KO_REACTION_NETWORK' --modelseed-dir '/mnt/cc061462-beb3-49ab-9318-5c7bf54d8588/database/MODELSEED' --overwrite-existing-network

A reaction network will be made from protein orthology annotations in the contigs database. Contigs database .............................: /mnt/b351004a-4dc6-4bcf-add3-21fc26707773/Eric_meta/GB_GCA_001567165_1.db

Reference KEGG KO database directory .........: /mnt/cc061462-beb3-49ab-9318-5c7bf54d8588/database/anvio-KEGG/KO_REACTION_NETWORK Reference ModelSEED database directory .......: /mnt/cc061462-beb3-49ab-9318-5c7bf54d8588/database/MODELSEED

METABOLIC REACTION NETWORK STATISTICS
Gene calls and KEGG Ortholog (KO) annotations
Total gene calls in genome ...................: 2,254 Genes annotated with protein KOs .............: 1,170 Genes in network .............................: 625 Protein KOs annotating genes .................: 991 KOs in network ...............................: 540
ModelSEED reactions in network and KO sources
Reactions in network .........................: 5,033 Mean reactions per KO ........................: 12.4 Stdev reactions per KO .......................: 34.5 Max reactions per KO .........................: 337

[16 Dec 23 21:21:54 Counting reactions from each alias source] ... /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3432: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:190: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:265: RuntimeWarning: Degrees of freedom <= 0 for slice ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in divide arrmean = um.true_divide(arrmean, div, out=arrmean, casting='unsafe', /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:257: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) Traceback (most recent call last): File "/home/e2s2/Softwares/anvio/bin/anvi-reaction-network", line 112, in main() File "/home/e2s2/Softwares/anvio/bin/anvi-reaction-network", line 29, in main constructor.make_network( File "/home/e2s2/Softwares/anvio/anvio/biochemistry/reactionnetwork.py", line 2412, in make_network network = self.make_contigs_database_network( File "/home/e2s2/Softwares/anvio/anvio/biochemistry/reactionnetwork.py", line 2757, in make_contigs_database_network stats['Max reactions per KEGG reaction'] = max_reactions_per_kegg_reaction = max(reaction_counts) ValueError: max() arg is an empty sequence

yqy6611 commented 8 months ago

Can someone please help me figure this out? Seems like this issue persists. Many thanks!

semiller10 commented 6 months ago

Sorry for the delay, @yqy6611. This should be fixed in the dev branch with https://github.com/merenlab/anvio/commit/cb8786a75ad7d441429e3b25176e41f57d8a4172. Try again after a git pull. I'm in the midst of major upgrades to the reaction network which I'll merge into the dev branch in the next few weeks.

yqy6611 commented 6 months ago

Sorry for the delay, @yqy6611. This should be fixed in the dev branch with cb8786a. Try again after a git pull. I'm in the midst of major upgrades to the reaction network which I'll merge into the dev branch in the next few weeks.

Hello Samuel @semiller10,

Thanks for your reply. Now I encountered another error:

A reaction network will be made from protein orthology annotations in the contigs database. Contigs database .............................: anvio/S1/S1_bin_1_orig.db

Reference KEGG KO database directory .........: /mnt/cc061462-beb3-49ab-9318-5c7bf54d8588/database/anvio-KEGG/KO_REACTION_NETWORK Reference ModelSEED database directory .......: /mnt/cc061462-beb3-49ab-9318-5c7bf54d8588/database/anvio-modelseed/MODELSEED [24 May 24 15:04:54 Counting reactions from each alias source] ... /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3432: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:190: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:265: RuntimeWarning: Degrees of freedom <= 0 for slice ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in divide arrmean = um.true_divide(arrmean, div, out=arrmean, casting='unsafe', /home/e2s2/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/numpy/core/_methods.py:257: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount)

METABOLIC REACTION NETWORK STATISTICS
Gene calls and KEGG Ortholog (KO) annotations Total gene calls in genome ...................: 2,250 Genes annotated with protein KOs .............: 1,602 Genes in network .............................: 860 Protein KOs annotating genes .................: 1,381 KOs in network ...............................: 752
ModelSEED reactions in network and KO sources Reactions in network .........................: 6,288 Mean reactions per KO ........................: 12.3 Stdev reactions per KO .......................: 32.6 Max reactions per KO .........................: 377
Reaction alias source comparison Reactions aliased by KEGG reaction ...........: 0 Reactions aliased by EC number ...............: 6,288 Rxns aliased by both KEGG rxn & EC number ....: 0 Reactions aliased only by KEGG reaction ......: 0 Reactions aliased only by EC number ..........: 6,288 KEGG reactions contributing to network .......: 0 Mean reactions per KEGG reaction .............: nan Stdev reactions per KEGG reaction ............: nan Max reactions per KEGG reaction ..............: 0 EC numbers contributing to network ...........: 712 Mean reactions per EC number .................: 9.4 Stdev reactions per EC number ................: 25.1 Max reactions per EC number ..................: 377
Reaction reversibility Reversible reactions .........................: 4,446 Irreversible reactions .......................: 1,842
Metabolites and localization Metabolites in network .......................: 4,464 Cytoplasmic metabolites ......................: 4,461 Extracellular metabolites ....................: 23 Exclusively cytoplasmic metabolites ..........: 4,441 Exclusively extracellular metabolites ........: 3 Cytoplasmic/extracellular metabolites ........: 20
Metabolite consumption and production Consumed metabolites .........................: 4,051 Produced metabolites .........................: 4,093 Both consumed & produced metabolites .........: 3,680 Exclusively consumed metabolites .............: 371 Exclusively produced metabolites .............: 413 Metabolites consumed or produced by 1 rxn ....: 1,897 Metabolites consumed or produced by 2 rxns ...: 1,095 Metabolites consumed or produced by 3+ rxns ..: 1,472

Traceback (most recent call last): File "/home/e2s2/Softwares/anvio/bin/anvi-get-metabolic-model-file", line 131, in main() File "/home/e2s2/Softwares/anvio/bin/anvi-get-metabolic-model-file", line 51, in main network: reactionnetwork.PangenomicNetwork = constructor.load_network( File "/home/e2s2/Softwares/anvio/anvio/biochemistry/reactionnetwork.py", line 5098, in load_network network = self.load_pan_database_network( File "/home/e2s2/Softwares/anvio/anvio/biochemistry/reactionnetwork.py", line 5475, in load_pan_database_network self_table = pan_db_info.get_self_table() File "/home/e2s2/Softwares/anvio/anvio/dbinfo.py", line 210, in get_self_table with DB(self.path, None, ignore_version=True) as database: AttributeError: 'ContigsDBInfo' object has no attribute 'path'

Do you know how to solve it? Many thanks!

merenlab / anvio