subprocess.CalledProcessError about sting

[ar0ch]

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

[xlinxlin]

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

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

[ar0ch]

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

[xlinxlin]

@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'

[ar0ch]

Great! 😄