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Error in load_gbk.py script when trying to load the genome LC789759 [Klebsiella pneumoniae](https://www.ncbi.nlm.nih.gov/nuccore/LC789759.1/).
```python
Traceback (most recent call last):
File "/…
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read_json almost never work for me. Here is for instance a json that is totally valid but breaks read_json
```
{
"id" : "GSM1698568",
"gse" : [
"GSE69360"
],
"title" : "Biochain_Adu…
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Hi, I need to build a custom database for my master thesis, but the problem is that, eventually, if I check the DB with the inspect function, it has "table size" equal to 0.
I followed the document…
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1. Use the taxid field of the UCSC JSON to create links like https://www.ncbi.nlm.nih.gov/datasets/taxonomy/5866
1. Make the species link to to the NCBI taxonomy page.
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Thank you very much for your powerful tools!
I ran into the following error while running the make_kreport.py script.
python make_kreport.py -i P1_S7_L001_R_kraken2.txt -t nt_ktaxonomy -o P1
…
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When running` datasets summary genome taxon "Bacillus" `or any other case where multiple taxa are under the same name, an error is returned, and the user is asked to use one of the taxids provided.
…
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I am hoping for some advice.
basically I want to classify my PE reads to Archaea, Bacteria, Eukaryote and Virus (d: domain with K: kingdom option being optimal) as to get an overview as to the % a…
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Hello everyone,
I was trying to build Krake2 databases with GTDB. However, since GTDB consists of only bacterial and archaeal sequences it would be ideal to build it along with the viral Refseq. Im n…
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In our current invocations in the WDL workflow, we run kraken, and then krona, on a bunch of samples to save on DB staging time and such. Currently, the krona portion is run in a for-loop after kraken…
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stats are here: https://docs.google.com/spreadsheets/d/14pe3pVfLay9FoNCOw_Bu58KcOMrlqq4lkgFFD3rAFXM/edit?gid=0#gid=0