add coverage disrupt the viewer image loading.

[yizhouc]

Hi, I am new to use blobtoolikt. I just start following the tutorial provided on the website. I am able to create the ASSEMBLY_NAME/blob and use a local instance to view the blob. When I add the busco data. it is fine. However, when I added the S_venezuelensis_HH1/DRR008460_cov.json (download as instructed). there is error message. however when try to use the viewer, I couldn't load the image anymore. The web page become blank.

[yizhouc]

There is typo. There is no error message when I added the --cov ~/blobtoolkit/blobtools2/blobtools add \ --cov ~/BTK_TUTORIAL/FILES/S_venezuelensis_HH1/DRR008460_cov.json \ ~/BTK_TUTORIAL/DATASETS/ASSEMBLY_NAME

[rjchallis]

Glad it seems to be working now. Just to clarify did you mean that you found a typo in the tutorial that I should fix, or was it in the command you had entered?

[yizhouc]

Thanks. It is a typo in my first message, where I missed the "no". in the sentence. Not in your tutorial. Here are some issues I have when I ran the tutorials, some maybe due to my lacking experience in this area. To install with conda, an extra run is needed for conda install r requirements.txt.

I am using OS ubuntu 18.04. I followed the steps in the tutorial, 1) to create the database is fine. I can use the viewer to load the scaffold statistic in the web browser. 2) add the BUSSO is fine, I can use the viewer and load the BUSCO statistics in the web page along with snail graph.
3) when I add -- cov, although there is no error message displayed in promot, the web page becomes blank. I repeated it twice, the results are the same. following are the command I used. ~/blobtoolkit/blobtools2/blobtools add --cov ~/BTK_TUTORIAL/FILES/S_venezuelensis_HH1/DRR008460_cov.json ~/BTK_TUTORIAL/DATASETS/ASSEMBLY_NAME 4) to add blast hit, the download ncbi.blastn.out, I got error "gzip: stdin: not in gzip format" curl https://blobtoolkit.genomehubs.org/download/ALIAS/S_v/S_venezuelensis_HH1/S_venezuelensis_HH1.blastn.nt.root.1.minus.6247.out.gz | gunzip -c > ASSEMBLY_NAME.ncbi.blastn.out

5) add the --hit for the diamond blatx.out file ~/blobtoolkit/blobtools2/blobtools add \ --hits ~/BTK_TUTORIAL/FILES/ASSEMBLY_NAME.diamond.blastx.out \ --taxrule bestsumorder \ --taxdump ~/databases/ncbi_taxdump \ ~/BTK_TUTORIAL/DATASETS/ASSEMBLY_NAME

Traceback (most recent call last): File "/home/yizhouc/blobtoolkit/blobtools2/lib/add.py", line 194, in main() File "/home/yizhouc/blobtoolkit/blobtools2/lib/add.py", line 152, in main meta=meta File "/home/yizhouc/blobtoolkit/blobtools2/lib/hits.py", line 525, in parse int(kwargs["--hit-count"]), File "/home/yizhouc/blobtoolkit/blobtools2/lib/hits.py", line 154, in bin_hits windows = set_windows(meta, taxrule) File "/home/yizhouc/blobtoolkit/blobtools2/lib/hits.py", line 117, in set_windows if "stats_windows" in meta.settings: AttributeError: settings

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This issue has being marked as dormant because viewer is being archived. The code is now part of the main BlobToolKit repository.

If you feel the issue has not been resolved, please follow the updated BlobToolKit installation instructions to first confirm that you are using the latest version, and then open a new issue at the main BlobToolKit repository if necessary.

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[github-actions[bot]]

This issue was closed because it has been inactive for 7 days since being marked as dormant.