Problems about Structure Display with anvi-display-structure about anvio

[meren]

Hi @YongyiPeng,

Can you please send the output for these two commands after running them in your anvi'o environment?

ls `python -c 'import anvio; import os; print(os.path.dirname(anvio.__file__))'`/data/interactive/lib/

ls `python -c 'import anvio; import os; print(os.path.dirname(anvio.__file__))'`/data/interactive/lib/bootstrap

[YongyiPeng]

Thanks for your quick reply!

I get these after running the first command:

JavaScript-MD5 bootstrap-sortable d3.js jquery-ui svg-crowbar
bootstrap bootstrap-waitingfor jquery marked toastr
bootstrap-markdown colpick jquery-svgpan randomColor treelib-js

After running the second command:
CNAME LICENSE bower.json docs js package.json
CONTRIBUTING.md README.md composer.json fonts less test-infra
Gruntfile.js _config.yml dist grunt package.js

[meren]

Can you please run this command and send the output:

ls `python -c 'import anvio; import os; print(os.path.dirname(anvio.__file__))'`/tests

[YongyiPeng]

The output is:
00.sh
init.py
pycache
misc
run_component_tests_for_SCVs_SAAVs_structure.sh
run_component_tests_for_SNVs.sh
run_component_tests_for_alons_classifier.sh
run_component_tests_for_cazymes.sh
run_component_tests_for_display_functions.sh
run_component_tests_for_export_locus.sh
run_component_tests_for_gene_level_stats.sh
run_component_tests_for_indels.sh
run_component_tests_for_inversions.sh
run_component_tests_for_manual_interactive.sh
run_component_tests_for_metabolism.sh
run_component_tests_for_metagenomics.sh
run_component_tests_for_minimal_metagenomics.sh
run_component_tests_for_pangenomics.sh
run_component_tests_for_trnaseq.sh
run_migration_tests_for_ancient_anvio_databases.sh
run_unit_tests_for_consensus_taxonomy.py
run_workflow_tests_for_all_workflows.sh
run_workflow_tests_for_contigs.sh
run_workflow_tests_for_ecophylo.sh
run_workflow_tests_for_metagenomics.sh
run_workflow_tests_for_metapangenomics.sh
run_workflow_tests_for_pangenomics.sh
run_workflow_tests_for_phylogenomics.sh
run_workflow_tests_for_sra_download.sh
sandbox
unit

[meren]

Good. Can you please run these two commands:

# change directory
cd `python -c 'import anvio; import os; print(os.path.dirname(anvio.__file__))'`/tests

# run test
./run_component_tests_for_SCVs_SAAVs_structure.sh new

At the end of this test, I get the following display on my browser, please let me know if you're getting the same exact error:

[YongyiPeng]

I get this error:

:: anvi-gen-structure-database with DSSP ...

Traceback for debugging

File "/opt/anaconda3/envs/anvio-8/bin/anvi-gen-structure-database", line 151, in
main(args)
File "/opt/anaconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/terminal.py", line 915, in wrapper
program_method(*args, **kwargs)
File "/opt/anaconda3/envs/anvio-8/bin/anvi-gen-structure-database", line 34, in main
structops.StructureSuperclass(args, create=True)._run()
File "/opt/anaconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/structureops.py", line 399, in init
self.dssp = DSSPClass(skip_sanity_check=self.skip_DSSP) # If we skip DSSP, skip sanity_check
File "/opt/anaconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/structureops.py", line 1084, in init
self.set_executable()
File "/opt/anaconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/structureops.py", line 1155, in set_executable
raise ConfigError("'mkdssp' or 'dssp' must be installed on your system, but "

Config Error: 'mkdssp' or 'dssp' must be installed on your system, but neither seem to appear
in your path :/ If you are certain you have either on your system (for instance
you can run either by typing 'mkdssp' or 'dssp' in your terminal window), you
may want to send a detailed bug report. If you want to install DSSP, check out
http://merenlab.org/2016/06/18/installing-third-party-software/#dssp. If you
want to skip secondary structure and solvent accessibility annotation, provide
the flag --skip-DSSP.

[meren]

Good. Please address this problem by following the instructions on the message until you don't see it anymore when you run ./run_component_tests_for_SCVs_SAAVs_structure.sh new in this directory.