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

[yqy6611]

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]

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

[semiller10]

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.

[yqy6611]

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!