failde run rhe script buidSpacedDB.sh

[Fengqing Wang]

Dear all,

I am new to use the CLARK-S. Firstly, I ran the ./set_targets.sh clark_db/ bacteria viruses fungi protozoa; Secondly, I ran the ./buidSpacedDB.sh, the error occurred. It said failed to find the database of discriminativa 31-mers or Please run the script  to define the targets. Could you show me where I did wrong? Thanks very much

[Rachid]

Hello Fengqing,

It seems the program did not find any existing database (a requirement for running CLARK-S). 

Please make sure to run the script "classify_metagenome.sh" first as described in the README file.

Let me know if this helps?

Thank you,

Best,

Rachid

[Fengqing Wang]

Dear Rachid,

Thanks for your reply. I tried several days. It's not successful now.

The ./buidSpacedDB.sh is successful, the ./classify_metagenome.sh -P 20180319.clean.R1.fa.gz 20180319.clean.R2.fa.gz -R 20180319_10.0+_clark_result.txt -m 0 -n 16 --gzipped is successful, however, there is no results after the ./estimate_abundance.sh. While I add the --spaced in "./classify_metagenome.sh -P 20180319.clean.R1.fa.gz 20180319.clean.R2.fa.gz -R 20180319_10.0+_clark_result.txt -m 0 -n 16 --gzipped --spaced", it said that "the program did not find the database for the provided reference sequences". I don,t know why. There are already the kmer file in the database file. I also don know where I can add the database to.

Thanks for your help.

All the best,

Fengqing

在 2020年8月4日星期二 UTC+2上午1:04:15，Rachid写道：

[Fengqing Wang]

Dear Rachid,

update:It's working now. Thanks

All the best,

Fengqing