q2-brocc create_local_taxonomy_db.py

Dear qiime 2 users,

I am trying to create a local database of the NCBI taxonomy using the “create_local_taxonomy_db.py” command from https://libraries.io/pypi/q2-brocc but gets an error. Can someone please help with fixing this error?

(qiime2-2019.10) [[email protected] bin]$ create_local_taxonomy_db.py
–2019-11-28 09:38:18-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
=> “/tmp/tmp963oxe2i/nucl_gb.accession2taxid.gz”
Resolving ftp.ncbi.nlm.nih.gov… 130.14.250.13, 2607:f220:41e:250::7
Connecting to 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 … 1892845083
==> PASV … done. ==> RETR nucl_gb.accession2taxid.gz … done.
Length: 1892845083 (1.8G) (unauthoritative)

100%[====================================>] 1,892,845,083 4.19M/s in 12m 58s

2019-11-28 09:51:20 (2.32 MB/s) - Control connection closed.
Retrying.

–2019-11-28 10:06:21-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
(try: 2) => “/tmp/tmp963oxe2i/nucl_gb.accession2taxid.gz”
Connecting to 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 … 1892845083
==> PASV … done. ==> REST 1892845083 … done.
==> RETR nucl_gb.accession2taxid.gz … done.

100%[+++++++++++++++++++++++++++++++++++++] 1,892,845,083 --.-K/s in 0s

2019-11-28 10:06:25 (0.00 B/s) - “/tmp/tmp963oxe2i/nucl_gb.accession2taxid.gz” saved [1892845083]

–2019-11-28 10:07:34-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
=> “/tmp/tmp963oxe2i/taxdump.tar.gz”
Resolving ftp.ncbi.nlm.nih.gov… 130.14.250.7, 2607:f220:41e:250::13
Connecting to ftp.ncbi.nlm.nih.gov|130.14.250.7|:21… connected.
Logging in as anonymous … Logged in!
==> SYST … done. ==> PWD … done.
==> TYPE I … done. ==> CWD (1) /pub/taxonomy … done.
==> SIZE taxdump.tar.gz … 50465665
==> PASV … done. ==> RETR taxdump.tar.gz … done.
Length: 50465665 (48M) (unauthoritative)

100%[======================================>] 50,465,665 191K/s in 4m 12s

2019-11-28 10:11:51 (196 KB/s) - “/tmp/tmp963oxe2i/taxdump.tar.gz” saved [50465665]

citations.dmp
delnodes.dmp
division.dmp
gencode.dmp
merged.dmp
names.dmp
nodes.dmp
gc.prt
readme.txt
Error: near line 1: disk I/O error
Error: near line 5: disk I/O error
Error: disk I/O error
Error: disk I/O error
Error: near line 14: disk I/O error
Error: near line 15: disk I/O error
Traceback (most recent call last):
File “/lustre/home/beng/miniconda3/envs/qiime2-2019.10/bin/create_local_taxonomy_db.py”, line 5, in
brocclib.taxonomy_db.main()
File “/lustre/home/beng/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/brocclib/taxonomy_db.py”, line 92, in main
init_db(database_fp, download_dir, accessions, nodes)
File “/lustre/home/beng/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/brocclib/taxonomy_db.py”, line 187, in init_db
subprocess.check_call([“sqlite3”, db], stdin=f, cwd=temp_dir)
File “/lustre/home/beng/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘[‘sqlite3’, ‘/lustre/home/beng/.brocc/taxonomy.db’]’ returned non-zero exit status 1.

Good afternoon,

Error: near line 15: disk I/O error

I think this could be your issue. Could you try running this command in a different location / folder and see if that improves it? :open_file_folder:

Colin

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