./set_targets.sh command not working

[jigyasa arora]

Hey All

I am trying to use CLARK-S for metagenome data analysis. According to the manual, I created an empty database folder and ran ./set_targets.sh command to download the bacterial and archaea RefSeq genomes.

But I am facing an error in the script.

 

Code- $set_targets.sh work/db bacteria --species

Error- Collecting metadata of bacteria... /home/j/jigyasa-arora/local/CLARKSCV1.2.5/set_targets.sh: line 91: ./make_metadata.sh: No such file or directory

Output- an empty targets.txt file

/home/j/jigyasa-arora/local/CLARKSCV1.2.5/ :is the location where I have downloaded the CLARK software and I have added the path to my bashrc file, so I can run it from anywhere.

When I try to run ./make_metadata.sh then-

Code- $make_metadata.sh db bacteria

Error- Selected directory not found. The program will create it.

Taxonomy data missing. The program will download data to bacteria/taxonomy.

/home/j/jigyasa-arora/local/CLARKSCV1.2.5/make_metadata.sh: line 54: ./download_taxondata.sh: No such file or directory

Failed to find taxonomy files. The program will try to download them...

/home/j/jigyasa-arora/local/CLARKSCV1.2.5/make_metadata.sh: line 58: ./download_taxondata.sh: No such file or directory

Failed to find taxonomy files.

The program must abort.

Output- It generates an empty bacteria file

[Rachid]

Hi Jigyasa,

Thank you for reporting this issue. I submitted a new fix and is now available in the CLARK website.

Could you please download the new package (date of today) and try to install again ?

Please let us know if this works,

Cheers,

Rachid 

[Shaina Morris]

Hi Rachid, 

I am using the newest version on the website (July 2019) and this error still exists. set_targets.sh tells me that make_metadata.sh does not exist. 

--Shaina

[Rachid]

Hi Shaina,

I am sorry you've encountered this error! I have rerun on my side using a fresh/new working directory and I encountered no issue.

Maybe you could provide more information/detail so I can reproduce your error?

Please could you download and install the latest version (V1.2.6.1) and try again in a manner that is similar the examples provided in the README file ?

Best,

Rachid