q2-brocc error about nt database import

I have also met a problem with brocc .

I have installed q2-brocc.I run the'blastn -query query.fasta -db mitogenomes -outfmt 7' code and I can get the hit result(mitogenomes is a customed nt database).

Then I run 'qiime brocc classify-brocc --i-query query.qza --o-classification query_brocc.qza' code and it returned 'BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/data1/WJJ02/YLB03/Software/Qiime2::]
'
Then I run 'qiime brocc classify-brocc --i-query query.qza --o-classification query_brocc.qza --p-blastdb mitogenomes' and it returned 'Did not detect a local copy of the NCBI taxonomy.Using NCBI EUtils to get taxonomic info instead.IndexError: list index out of range
'
and my nt folder including 'nhr','nin','nsq' files and so on.

Could you please help me?

(qiime2-2020.6) [[email protected] library]$ create_local_taxonomy_db.py
--2022-02-24 12:58:24-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
=> ‘/tmp/tmp0clvnrp_/nucl_gb.accession2taxid.gz’
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.13, 130.14.250.12, 2607:f220:41e:250::13, ...
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.13|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /pub/taxonomy/accession2taxid ... done.
==> SIZE nucl_gb.accession2taxid.gz ... 2161740998
==> PASV ... done. ==> RETR nucl_gb.accession2taxid.gz ... done.
Length: 2161740998 (2.0G) (unauthoritative)

nucl_gb.accession2taxid.gz 100%[================================================================================>] 2.38G 568KB/s in 60m 34s

2022-02-24 13:59:02 (687 KB/s) - Control connection closed.
Retrying.

--2022-02-24 14:14:03-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
(try: 2) => ‘/tmp/tmp0clvnrp_/nucl_gb.accession2taxid.gz’
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.13|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /pub/taxonomy/accession2taxid ... done.
==> SIZE nucl_gb.accession2taxid.gz ... 2161740998
==> PASV ... done. ==> REST 2557951762 ... done.
==> RETR nucl_gb.accession2taxid.gz ...
No such file ‘nucl_gb.accession2taxid.gz’.

Traceback (most recent call last):
File "/data1/WJJ02/.conda/envs/qiime2-2020.6/bin/create_local_taxonomy_db.py", line 5, in
brocclib.taxonomy_db.main()
File "/data1/WJJ02/.conda/envs/qiime2-2020.6/lib/python3.6/site-packages/brocclib/taxonomy_db.py", line 83, in main
accession_fp = download_accessions(download_dir)
File "/data1/WJJ02/.conda/envs/qiime2-2020.6/lib/python3.6/site-packages/brocclib/taxonomy_db.py", line 103, in download_accessions
["wget", "--directory-prefix", download_dir, ACCESSION_URL])
File "/data1/WJJ02/.conda/envs/qiime2-2020.6/lib/python3.6/subprocess.py", line 311, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['wget', '--directory-prefix', '/tmp/tmp0clvnrp_', 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz']' returned non-zero exit status 8.

The above is the error information.Could you help me?

Hi,Kyle.I have also met a problem with brocc .

I have installed q2-brocc.I run the'blastn -query query.fasta -db mitogenomes -outfmt 7' code and I can get the hit result(mitogenomes is a customed nt database).

Then I run 'qiime brocc classify-brocc --i-query query.qza --o-classification query_brocc.qza' code and it returned 'BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/data1/WJJ02/YLB03/Software/Qiime2::]
'
Then I run 'qiime brocc classify-brocc --i-query query.qza --o-classification query_brocc.qza --p-blastdb mitogenomes' and it returned 'Did not detect a local copy of the NCBI taxonomy.Using NCBI EUtils to get taxonomic info instead.IndexError: list index out of range
'
and my nt folder including 'nhr','nin','nsq' files and so on.

Could you please help me?

Hi @YLB ,
Please see the Code of Conduct - QIIME 2 Forum

Particularly the parts about "Be Patient", "Keep it Tidy" and "Cross Posting".

You have posted a couple duplicate questions, and a related question about brocc within 24hr... please slow down and wait for a response. Additional cross-posting etc will lead to your account being temporarily locked to prevent uncontrolled posting, so please be patient and try to work through one problem at a time.

q2-brocc is developed by a different group, does not seem to be actively developed, and might not be supported on the QIIME 2 forum (we have not seen @kylebittinger for a few years on here). brocc itself is a stand-alone program, not part of QIIME 2, so questions about brocc itself should be filed elsewhere. What I am trying to say is that brocc/q2-brocc might have a different support platform (you should check their documentation).

Thanks for your reply.Do you know q2-brocc support platform?

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