The “fake” database seems to be incomplete #96
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Maxim,
You are correct, I haven’t provided the “fake” database in a long time (I’m actually surprised you were able to find it!). Is it critical for what you need to do? I generally recommend against trying to build your own database and encourage you to use the one we provide.
Jeff
=======================
Jeff Bowman
Associate Professor
Scripps Institution of Oceanography
www.polarmicrobes.org
From: Maxim Sikolenko ***@***.***>
Sent: Thursday, February 9, 2023 1:10 AM
To: bowmanjeffs/paprica ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [bowmanjeffs/paprica] The “fake” database seems to be incomplete (Issue #96)
Hello!
It seems that the “fake” ref_genome_database.tgs archive is incomplete: it lacks file(s) of 23S rRNA sequences.
And here is why I think so.
I’m trying to build a custom database for paprica. So I follow the tutorial <https://urldefense.com/v3/__https:/www.polarmicrobes.org/building-the-paprica-database/__;!!Mih3wA!DpgfImjzkfFJD9zTyS61-6FKyl_QRqS_UXl-H0twKVamlTFyDs79UKo_Is2yzRvQKdZ3plTVnC4od46PZ2roIl3TjQ$> : I downloaded the “fake” mini-database <https://urldefense.com/v3/__http:/www.polarmicrobes.org/extras/ref_genome_database.tgz__;!!Mih3wA!DpgfImjzkfFJD9zTyS61-6FKyl_QRqS_UXl-H0twKVamlTFyDs79UKo_Is2yzRvQKdZ3plTVnC4od46PZ2rFBYdj8w$> , untarred it and ran paprica-make_ref.py (I use paprica v0.7.2):
./paprica-make_ref.py \
-ref_dir ref_genome_database \
-download test \
-domain bacteria \
-cpus 4
And here is the output:
Checking for reference database directories, will create if necessary...
[Parallel(n_jobs=-1)]: Using backend LokyBackend with 8 concurrent workers.
Checking files for accession /mnt/1.5_drive_0/tmp/paprica_sandbox/fake_db/ref_genome_database/bacteria/refseq/GCF_000007485.1
# [... checking more files, skip it ...]
Checking files for accession /mnt/1.5_drive_0/tmp/paprica_sandbox/fake_db/ref_genome_database/bacteria/refseq/GCF_001314225.1
[Parallel(n_jobs=-1)]: Done 4 out of 10 | elapsed: 1.0s remaining: 1.5s
[Parallel(n_jobs=-1)]: Done 7 out of 10 | elapsed: 1.0s remaining: 0.4s
[Parallel(n_jobs=-1)]: Done 10 out of 10 | elapsed: 1.2s remaining: 0.0s
[Parallel(n_jobs=-1)]: Done 10 out of 10 | elapsed: 1.2s finished
[Parallel(n_jobs=-1)]: Using backend LokyBackend with 8 concurrent workers.
[Parallel(n_jobs=-1)]: Done 0 out of 0 | elapsed: 0.0s finished
[Parallel(n_jobs=-1)]: Using backend LokyBackend with 8 concurrent workers.
[Parallel(n_jobs=-1)]: Done 0 out of 0 | elapsed: 0.0s finished
Traceback (most recent call last):
File "./paprica-make_ref.py", line 736, in <module>
for record in SeqIO.parse(ref_dir_domain + 'refseq/' + d + '/' + d + '.23S.fasta', 'fasta'):
File "/home/cager/Misc_soft/py-venv/lib/python3.8/site-packages/Bio/SeqIO/__init__.py", line 607, in parse
return iterator_generator(handle)
File "/home/cager/Misc_soft/py-venv/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
super().__init__(source, mode="t", fmt="Fasta")
File "/home/cager/Misc_soft/py-venv/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 47, in __init__
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/1.5_drive_0/tmp/paprica_sandbox/fake_db/ref_genome_database/bacteria/refseq/GCF_000007485.1/GCF_000007485.1.23S.fasta'
I see in paprica-make_ref.py:check_directory that the script checks if a file *23S.fasta exists (line 387). And if some required files don’t exist, the whole directory gets removed (lines 399-400). Indeed, after I run paprica-make_ref.py, all GCF_* directories in ref_genome_database/bacteria/refseq/ become empty.
And indeed, in a freshly downloaded ref_genome_database/bacteria/refseq/, all GCF_* directories don’t contain a file ending with 23S.fasta.
Is the archive really misconfigured? Or I’m getting something wrong?
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Not really.
Okay, I’ll just get along without it. Thank you, Jeff! |
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Hello!
It seems that the “fake”
ref_genome_database.tgsarchive is incomplete: it lacks file(s) of 23S rRNA sequences.And here is why I think so.
I’m trying to build a custom database for paprica. So I follow the tutorial: I downloaded the “fake” mini-database, untarred it and ran
paprica-make_ref.py(I use paprica v0.7.2):And here is the output:
I see in
paprica-make_ref.py:check_directorythat the script checks if a file*23S.fastaexists (line 387). And if some required files don’t exist, the whole directory gets removed (lines 399-400). Indeed, after I runpaprica-make_ref.py, allGCF_*directories inref_genome_database/bacteria/refseq/become empty.And indeed, in a freshly downloaded
ref_genome_database/bacteria/refseq/, allGCF_*directories don’t contain a file ending with23S.fasta.Is the archive really misconfigured? Or I’m getting something wrong?
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