BlastN "no high coverage hits

[NailouZhang]

hi Mike,

I met the same as Issue #22. I install krona with mamba. Then I successfully updated the Kron database using the following code.

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

the blast result is always "no high coverage hits" when I used known virus download from NCBI (e.g. ZIKV, sars-cov2, TBEV).

My command python run_cenote-taker2.py --run_title ZNLtest -c testVirus.fasta -m 260 -t 45 -p False -db standard -am True --molecule_type RNA --known_strains blast_knowns --blastn_db ~/nt/nt --minimum_length_linear 1000 --lin_minimum_hallmark_genes 1 -hh hhsearch --hallmark_taxonomy True

ktClassifyBLAST -o test1.tab ZNLtest3.blastn_intraspecific.out Loading taxonomy... Classifying ZNLtest3.blastn_intraspecific.out... [ WARNING ] "ZNLtest3.blastn_intraspecific.out" had e-values of 0. Approximated log[10] of 0 as -450. [ WARNING ] The following accessions look strange and may yield erroneous results. Please check if they are acual valid NCBI accessions: tname [ WARNING ] The following accessions were not found in the local database (if they were recently added to NCBI, use updateAccessions.sh to update the local database): tname Writing test1.tab...

To import, run: ktImportTaxonomy test1.tab # This can also work well

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How can I resolve this issue?

[mtisza1]

Hi Nailou,

Thank you for opening this issue. I notice that you are using a version of Cenote-Taker 2 that uses thekronatools commands. The newest version of Cenote-Taker 2 (v2.1.5) uses taxonkit instead which solves most/all of these errors. Is it possible for you to update to v2.1.5? If you need to use the older version (that you are currently on) for reproducibilty purposes, I can look closer at your issue.

Let me know,

Mike

[NailouZhang]

Hi Mike,

I install Cenote-Taker 2 (v2.1.5) with git clone --recursive https://github.com/mtisza1/Cenote-Taker2.git I check the difference between cenote-taker2.1.3.sh and cenote-taker2.1.5.sh, I think this led to this issue.

"" ktClassifyBLAST -o '${circle%.rotate.fasta}.tax_guide.blastn.tab ${circle%.rotate.fasta}.blastn_intraspecific.out >/dev/null 2>&1 taxid=$( grep -v "qname" ${circle%.rotate.fasta}.tax_guide.blastn.tab | tail -n+2 | head -n1 | cut -f2 ) ""

# in cenote-taker2.1.3.sh here tname->taxid->ORGANISM_H. "tname" in ${circle%.rotate.fasta}.blastn_intraspecific.out "taxid" in ${circle%.rotate.fasta}.tax_guide.blastn.tab #

# in cenote-taker2.1.5.sh here tname->ORGANISM_H->taxid. ORGANISM_H=$( head -n2 ${circle%.rotate.fasta}.blastn_intraspecific.out | tail -n1 | sed 's/[/&\n/;s/.\n//;s/]/\n&/;s/\n.//' ) taxid=$( grep " | ${ORGANISM_H} | " ${CENOTE_DBS}/taxdump/names.dmp | head -n1 | cut -f1 ) #

[NailouZhang]

Hi Mike,

It works well with cenote-taker2.1.3.sh. But some known viruses (e.g. SARS-Cov2) were input into Cenote-Taker2 for validation, but show no high coverage hits.