The GTDB-Tk reference data does not exist or is corrupted.

[vichy123]

hello,I have installed GTDB-Tk v2.3.2 and downloaded the datasets release214 ,also have set GTDBTK_DATA_PATH ,but it also displayed that"The GTDB-Tk reference data does not exist or is corrupted. "

gtdbtk check_install
[2024-05-09 14:57:20] INFO: GTDB-Tk v2.3.2
[2024-05-09 14:57:20] INFO: gtdbtk check_install

================================================================================
ERROR

---

      The 'GTDBTK_DATA_PATH' environment variable is not defined.           

        Please set this variable to your reference data package.            
       https://ecogenomics.github.io/GTDBTk/installing/index.html           

================================================================================
[2024-05-09 14:57:20] ERROR: Controlled exit resulting from early termination.
(metachip2env) adruan@adruan-Precision-7820-Tower:$ conda env config vars set GTDBTK_DATA_PATH="/newdisk/metabolic/db/release214"
To make your changes take effect please reactivate your environment

Vichy:
gtdbtk check_install
[2024-05-09 21:09:06] INFO: GTDB-Tk v2.3.2
[2024-05-09 21:09:06] INFO: gtdbtk check_install

================================================================================
ERROR

---

       The GTDB-Tk reference data does not exist or is corrupted.           
           GTDBTK_DATA_PATH=~/newdisk/metabolic/db/release214               

Please compare the checksum to those provided in the download repository.
https://github.com/Ecogenomics/GTDBTk#gtdb-tk-reference-data

[2024-05-09 21:09:06] ERROR: Controlled exit resulting from early termination.

[pchaumeil]

Hello,
Are you storing the GTDB-Tk database in your home directory?

If you use the tilt key (~) during the export of your environment variable do not use double quotes
GTDBTK_DATA_PATH=~/newdisk/metabolic/db/release214

But I would recommend exporting the full path to the database:
GTDBTK_DATA_PATH=/path/to/your/homedirectory/newdisk/metabolic/db/release214

Regards,
Pierre

[vichy123]

Oh,thanks,it has been working now,that's an unexpected error. 

…

------------------ 原始邮件 ------------------ 发件人: "Ecogenomics/GTDBTk" ***@***.***>; 发送时间: 2024年5月10日(星期五) 上午6:06 ***@***.***>; ***@***.******@***.***>; 主题: Re: [Ecogenomics/GTDBTk] The GTDB-Tk reference data does not exist or is corrupted. (Issue #588) Hello, Are you storing the GTDB-Tk database in your home directory? If you use the tilt key (~) during the export of your environment variable do not use double quotes GTDBTK_DATA_PATH=~/newdisk/metabolic/db/release214 But I would recommend exporting the full path to the database: GTDBTK_DATA_PATH=/path/to/your/homedirectory/newdisk/metabolic/db/release214 Regards, Pierre — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Arkadiy-Garber]

I am getting the same error:

(base) ark@TheBelly:~/bin/GTDBTk/data$ gtdbtk 

================================================================================
                                     ERROR                                      
________________________________________________________________________________

           The GTDB-Tk reference data does not exist or is corrupted.           
                   GTDBTK_DATA_PATH=/home/ark/bin/GTDBTk/data                   

   Please compare the checksum to those provided in the download repository.    
          https://github.com/Ecogenomics/GTDBTk#gtdb-tk-reference-data          
================================================================================



(base) ark@TheBelly:~/bin/GTDBTk/data$ ls
ar53_marker_genes_all_r220  ar53.tree.gz                  citations.dmp          gtdb_vs_ncbi_archaea.xlsx   METHODS.txt                 sp_clusters.tsv
ar53_metadata.tsv.gz        bac120_marker_genes_all_r220  delnodes.dmp           gtdb_vs_ncbi_bacteria.xlsx  names.dmp                   synonyms.ar53.tsv
ar53_msa_marker_info.tsv    bac120_metadata.tsv.gz        division.dmp           hq_mimag_genomes.tsv        ncbi_vs_gtdb_archaea.xlsx   synonyms.bac120.tsv
ar53_msa_mask.txt           bac120_msa_marker_info.tsv    FILE_DESCRIPTIONS.txt  images.dmp                  ncbi_vs_gtdb_bacteria.xlsx  VERSION.txt
ar53.sp_labels.tree         bac120_msa_mask.txt           gc.prt                 individual                  nodes.dmp
ar53_taxonomy.tsv           bac120.sp_labels.tree         gencode.dmp            MD5SUM.txt                  qc_failed.tsv
ar53_taxonomy.tsv.gz        bac120_taxonomy.tsv           gtdb.dic               merged.dmp                  readme.txt
ar53.tree                   bac120.tree                   gtdbtk_package         metadata_field_desc.tsv     RELEASE_NOTES.txt

Is there something missing from this directory?

[pchaumeil]

Hello,
Please read the documentation about downloading the GTDB-Tk package:

https://ecogenomics.github.io/GTDBTk/installing/index.html#gtdb-tk-reference-data

You do not need to download all files from the GTDB website, only the GTDB-Tk archive.