Closed yizhouc closed 1 year ago
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
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?
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
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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.