Problems about Structure Display with anvi-display-structure

[YongyiPeng]

Hi, thanks for developing this powerful tool! I appreciate for its exceptional performance, but I encountered a specific issue while attempting to display structure (anvio's interactive stuck at still loading).

Anvio's version Anvi'o .......................................: marie (v8) Python .......................................: 3.10.13

Profile database .............................: 38 Contigs database .............................: 21 Pan database .................................: 16 Genome data storage ..........................: 7 Auxiliary data storage .......................: 2 Structure database ...........................: 2 Metabolic modules database ...................: 4 tRNA-seq database ............................: 2

System info masOS high sierra 10.13.2

Detailed description anvi-display-structure -c CONTIGS.db -p PROFILE.db -s STRUCTURE_889488.db --gene-caller-ids 889488

The output is:

• The server is up and running 🎉

WARNING

If you are using OSX and if the server terminates prematurely before you can see anything in your browser, try running the same command by putting 'sudo ' at the beginning of it (you will be prompted to enter your password if sudo requires super user credentials on your system). If your browser does not show up, try manually entering the URL shown below into the address bar of your favorite browser. cough CHROME cough.

Server address ...............................: http://0.0.0.0:8080

• When you are ready, press CTRL+C once to terminate the server and go back to the command line.

The website loads into the Chrome browser, but it remains stuck in a continuous loading state.

Messages in the console of Chrome Developer tools Failed to load resource: net::ERR_CONNECTION_RESET bootstrap-slider.css:1 Failed to load resource: net::ERR_CONNECTION_RESET bootstrap-slider.min.js:1 Failed to load resource: net::ERR_CONNECTION_RESET d3.min.js:1 Failed to load resource: net::ERR_CONNECTION_RESET jszip.min.js:1 Failed to load resource: net::ERR_CONNECTION_RESET FileSaver.js:1 Failed to load resource: net::ERR_CONNECTION_TIMED_OUT ngl.js:1 Uncaught TypeError: structure.js?rand=edf3395fa85040d922fbaf29cb276773:1134 $(...).slider is not a function at structure.js?rand=edf3395fa85040d922fbaf29cb276773:1134:43 at Array.forEach (<anonymous>) at Object.success (structure.js?rand=edf3395fa85040d922fbaf29cb276773:1105:25) at j (jquery.js:3148:30) at Object.fireWith [as resolveWith] (jquery.js:3260:7) at x (jquery.js:9314:14) at XMLHttpRequest.b (jquery.js:9718:8) Uncaught (in promise) ReferenceError: NGL is not defined structure.js?rand=edf3395fa85040d922fbaf29cb276773:255 at create_single_ngl_view (structure.js?rand=edf3395fa85040d922fbaf29cb276773:255:17) at create_ngl_views (structure.js?rand=edf3395fa85040d922fbaf29cb276773:225:15) at load_sample_group_widget (structure.js?rand=edf3395fa85040d922fbaf29cb276773:191:9) at HTMLSelectElement.<anonymous> (structure.js?rand=edf3395fa85040d922fbaf29cb276773:95:9) at HTMLSelectElement.dispatch (jquery.js:4670:9) at r.handle (jquery.js:4338:28) at Object.trigger (jquery.js:4579:12) at HTMLSelectElement.<anonymous> (jquery.js:5289:17) at Function.each (jquery.js:384:23) at m.fn.init.each (jquery.js:136:17)

I have used different ip address and port numbers, but it didn't help. I would be grateful if you could provide any suggestion.

[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.