# mismatch between taxonomy and sequence data that download from NCBI using qiime rescript get-ncbi-data
**URL:** https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130
**Category:** Technical Support
**Tags:** taxonomy, ncbi, rescript
**Created:** [May 13, 2025, 10:32am UTC](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130 "2025-05-13T10:32:19Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@Si\_Vivy](https://forum.qiime2.org/u/Si_Vivy)
#### Post date: [May 13, 2025, 10:32am UTC](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130/1 "2025-05-13T10:32:19Z")
Hello !
I am trying to download COI data from NCBI with this code:
```css
qiime rescript get-ncbi-data \
--p-query '(cytochrome c oxidase subunit I[gene] OR cytochrome oxidase subunit 1[gene] OR cytochrome oxidase subunit I[gene] OR COX1[gene] OR CO1[gene] OR COI[gene] OR COXI[gene] NOT environmental sample[Title] NOT environmental samples[Title] NOT environmental[Title] NOT uncultured[Title] NOT unclassified[Title] NOT unidentified[Title] NOT unverified[Title] NOT txid2[ORGN] NOT txid2157[ORGN] NOT txid10239[ORGN])' \
--verbose --p-logging-level INFO \
--p-n-jobs 8 \
--o-sequences CO1_sequences.qza \
--o-taxonomy CO1_taxonomy.qza
```
And then I export CO1\_sequences.qza, and CO1\_taxonomy.qza using the code below:
```css
qiime tools export \
--input-path CO1_sequences.qza \
--output-path exported-seq-co1
qiime tools export \
--input-path CO1_taxonomy.qza \
--output-path exported-taxonomy-co1
```
Subsequently, I converted the .fasta file in the exported-seq-co1 folder to .tsv format and compared it with the taxonomy data in the exported-taxonomy-co1 folder. I discovered that not all sequence IDs (accessions) present in CO1\_sequences are found in CO1\_taxonomy, and I am uncertain about the reason for this discrepancy.
Thanks for helping me!
---
### Author:  [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [May 13, 2025, 1:46pm UTC](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130/2 "2025-05-13T13:46:14Z")
Hi @Si_Vivy,
Thank you for providing your commands. Very helpful! 🙂
This thread may help explain the issue:
> [@dereplication error with data collected from \`get-ncbi-data\` command](https://forum.qiime2.org/t/dereplication-error-with-data-collected-from-get-ncbi-data-command/16164):
>
> A collection of sequence and taxonomy data were obtained running @BenKaehler's fantastic get-ncbi-data command within [RESCRIPt](https://forum.qiime2.org/t/using-rescript-to-compile-an-sequence-databases-and-taxonomy-classifiers-from-ncbi-genbank/15947). Raw sequence data collected from get-ncbi-data are [available here](https://osf.io/khup2/) Raw taxonomy data collected from get-ncbi-data are [available here](https://osf.io/wbd63/) I had intended on filtering and dereplicating these sequences using a series of RESCRIPt commands: cull-seqs and filter-seqs-length to filter, and dereplicate to ... well, dereplicate. While the filtering commands completed successfully…
-Mike
---
### Author:  [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [May 13, 2025, 3:52pm UTC](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130/3 "2025-05-13T15:52:15Z")
Hi @Si_Vivy,
I was able to successfully run your command without issue via QIIME 2 version `2025.4`. That is, both files contained the same IDs.
I ran:
```auto
qiime rescript get-ncbi-data \
--p-query '(cytochrome c oxidase subunit I[gene] OR cytochrome oxidase subunit 1[gene] OR cytochrome oxidase subunit I[gene] OR COX1[gene] OR CO1[gene] OR COI[gene] OR COXI[gene] NOT environmental sample[Title] NOT environmental samples[Title] NOT environmental[Title] NOT uncultured[Title] NOT unclassified[Title] NOT unidentified[Title] NOT unverified[Title] NOT txid2[ORGN] NOT txid2157[ORGN] NOT txid10239[ORGN])' \
--verbose --p-logging-level INFO \
--p-n-jobs 8 \
--o-sequences CO1_sequences.qza \
--o-taxonomy CO1_taxonomy.qza
```
Then I was able to successfully run the following command. Which should fail if the IDs between the two do not match :
```auto
qiime rescript dereplicate \
--i-sequences CO1_sequences.qza \
--i-taxa CO1_taxonomy.qza \
--p-threads 10 \
--output-dir CO1_derep \
--verbose
```
To further ensure that the files contained the same information in both the sequence and taxonomy files I ran the following:
```auto
qiime tools export \
--input-path CO1_sequences.qza \
--output-path CO1_sequences_export
qiime tools export \
--input-path CO1_taxonomy.qza \
--output-path CO1_taxonomy_export
# grab IDs and save to file
cat CO1_sequences_export/dna-sequences.fasta | egrep '^>' | sed 's/>//' > seq_ids.txt
cat CO1_taxonomy_export/taxonomy.tsv | tail -n +2 | cut -d $'\t' -f 1 > tax_ids.txt
# run diff to see if there are any differences (the IDs should be in the same order):
diff seq_ids.txt tax_ids.txt
```
The diff command revealed no differences between the IDs in the FASTA and Taxonomy files. I am guessing that there was a network issue, or something that caused the files to files to be incomplete, and/or the version of QIIME 2 / RESCRIPt is an older version? 🤷♂️
---
### Author:  [@Si\_Vivy](https://forum.qiime2.org/u/Si_Vivy)
#### Post date: [May 19, 2025, 7:58am UTC](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130/4 "2025-05-19T07:58:44Z")
Hi Mike,
Thanks so much for your reply; the problem was solved when I used version 2025.4.
vivy
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [June 19, 2025, 1:59pm UTC](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130/5 "2025-06-19T13:59:12Z")
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