Problem running buildSpacedDB.sh

[Kate]

Hey everyone,

I'm trying to run CLARK-S on eight shotgun sequences, following the steps laid out in the "Overview" on clark.cs.ucr.edu. I have the database imported, and then ran the following commands with the following outputs:

kate@:~/May2019/assembled$ ../../git/CLARKSCV1.2.6.1/./set_targets.sh ../../git/AllDB bacteria plasmid plastid --species
Collecting metadata of bacteria... done.
Collecting metadata of plasmid... done.
Collecting metadata of plastid... done.
kate@:~/May2019/assembled$ ../../git/CLARKSCV1.2.6.1/./classify_metagenome.sh -O assSamp.txt -R assOut.txt
CLARK version 1.2.6.1 (UCR CS&E. Copyright 2013-2019 Rachid Ounit, rouni001@cs.ucr.edu)
The program did not find the database files for the provided settings and reference sequences (8110 targets). The program will build them.
Starting the creation of the database of targets specific 31-mers from input files...
 Progress report: (31061/31061)    59688730684 nt read in total.
Mother Hashtable successfully built. 19040622255 31-mers stored.
Hashtable sorting done: maximum number of collisions: 40
Removal of common k-mers done: 17019029262 specific 31-mers found.
Creating database in disk...
17019029262 31-mers successfully stored in database.
Loading database [../../../git/AllDB//bacteria_plasmid_plastid_0/db_central_k31_t8110_s1610612741_m0.tsk.*] ...
Loading done (database size: 103724 MB read, with sampling factor 2)
Mode: Default using 1 CPU.

(Then it successfully processed all of my files).

Now, when I try to run buildSpacedDB.sh, I get the following error: 

kate@:~/May2019/assembled$ ../../git/CLARKSCV1.2.6.1/./buildSpacedDB.sh
Please run the script set_targets.sh to define the targets.

I've tried rerunning set_targets.sh, which produces the same results. What am I doing wrong here? Any help would be great. Thanks,

-Kate

[Rachid]

Hi Kate,

Thank you for your interest and using the CLARK tools.

You should invoke the "buildSpacedDB.sh" script from the CLARK working directory.

So from your directory: ~/May2019/assembled, do the following:

$ cd ../../git/CLARKSCV1.2.6.1/./

$ ./buildSpacedDB.sh

Best,

Rachid

[Rachid]

Hi Kate,

Please let me know whether this answer helped?

Thank you,

Rachid