BlastN "no high coverage hits" about cenote-taker2

[mtisza1]

Hi Matthijs,

Thank you for opening this issue.

First, let me apologize for the delay in replying. I've been extremely busy lately, and I've had to decide to not reply to Cenote-Taker 2 issues temporarily. I will be "back" to quick responses and updates(!) at the end of February.

I looked at your log and I can't see anything funny going on. Based on what you said, BLASTN ran and produced the appropriate alignments. I think the "no high coverage hits" could be occurring if your installation of the krona databases didn't work or if efetch is not properly connecting to the NCBI server.

To check if the krona database is installed, activate the cenote-taker2_env and find any file ending in .blastn_intraspecific.out (e.g. in the DTR_contigs_with_viral_domain of your output). Input a command like so:

ktClassifyBLAST -o test1.tab test_blastn_1ct2.blastn_intraspecific.out

If this doesn't work, you'll have to install/update the krona databases. Change to the main Cenote-Taker2 directory and use these commands (This requires at least 4 CPUs for some reason and will take 20-40 minutes, so please have those resources available):

KRONA_DIR=$( which python | sed 's/bin\/python/opt\/krona/g' )
cd ${KRONA_DIR}
sh updateTaxonomy.sh
cd ${KRONA_DIR}
sh updateAccessions.sh

To check efetch, activate the cenote-taker2_env and input this command:

efetch -db taxonomy -id 133704 -format xml | xtract -pattern Taxon -block "*/Taxon" -tab "\n" -element TaxId,ScientificName,Rank

Other explanations are possible, however, and you can email a compressed file of the output directory of the test run to inspect.

best,

Mike

[M-K1]

Hey Mike,

Thanks for your advise, running updateTaxonomy.sh and updateAccessions.sh of the cenote-taker2 conda environment allowed me to correctly get BLASTn outputs. Another thing I'm wondering is what the ORGANISM_NAME is based on, as I have searched the usual databases and I couldn't find a match. Can you tell me what these names are based on?

Thx,

Matthijs