Comments (5)
Ah, this is a bug in db_util.py
that we didn't catch when making config paths relative. Could you give the version of db_util.py
I just pushed a try
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Ah, this is a bug in
db_util.py
that we didn't catch when making config paths relative. Could you give the version ofdb_util.py
I just pushed a try
The version number is 1.2
(base) mkzhouy1@supermicro:~$ ~/git/STing/scripts/db_util.py --version
db_util.py
version: 1.2
last update: 11/14/2019
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I just didn't bump the version (just pushed that too)
db_util.py --version
db_util.py
version: 1.2.1
last update: 07/09/2020
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@ar0ch Now it works, thank you!
(base) mkzhouy1@supermicro:/mnt/data/2007-mlst-silke/STing_demo$ ~/git/STing/scripts/db_util.py fetch --query "Neisseria spp." --out_dir my_dbs --build_index
Database: "Neisseria spp."
Fetching allele sequences:
- https://pubmlst.org/data/alleles/neisseria/abcZ.tfa -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/abcZ.fa
- https://pubmlst.org/data/alleles/neisseria/adk.tfa -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/adk.fa
- https://pubmlst.org/data/alleles/neisseria/aroE.tfa -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/aroE.fa
- https://pubmlst.org/data/alleles/neisseria/fumC.tfa -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/fumC.fa
- https://pubmlst.org/data/alleles/neisseria/gdh.tfa -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/gdh.fa
- https://pubmlst.org/data/alleles/neisseria/pdhC.tfa -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/pdhC.fa
- https://pubmlst.org/data/alleles/neisseria/pgm.tfa -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/pgm.fa
Fetching profiles:
- https://pubmlst.org/data/profiles/neisseria.txt -> /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/profile.txt
Building STing index:
/home/mkzhouy1/git/STing/bin/indexer -c /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/config.txt -p /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/db/index
Loading sequences from sequences files:
N Loci #Seqs. File
1 abcZ 1077 /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/abcZ.fa
2 adk 840 /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/adk.fa
3 aroE 1118 /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/aroE.fa
4 fumC 1184 /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/fumC.fa
5 gdh 1156 /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/gdh.fa
6 pdhC 1096 /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/pdhC.fa
7 pgm 1172 /mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/pgm.fa
Total sequences loaded: 7643
Loading the profiles file... Done!
Creating and saving ESA index from loaded sequences... Done!
Index created successfully with prefix '/mnt/data/2007-mlst-silke/STing_demo/my_dbs/neisseria_spp/db/index'
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Great! 😄
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Related Issues (15)
- Rewrite git history for publication
- Could not open the input file 'ERR026529_1.fastq.gz' HOT 3
- cgMLST schemes? HOT 21
- finding rST through rMLST scheme HOT 2
- Profile file for cgMLST HOT 3
- indexer reports "ERROR: The config file does not contain the [loci] section." HOT 1
- Preparing the database missing from README
- Is it possible to use assembly instead of NGS raw reads?
- Check licensing info HOT 1
- Automated STing MLST db
- Indexer throwing ParseError HOT 2
- Proper usage of index HOT 4
- db_util.py not able to download data from PubMLST HOT 1
- Missing files HOT 2
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