the website to download ssu.fna for GTDB doesn't work

[zhou-sumei]

Dear developer, I'm using the GTDB database to assign the taxonomic label for my contigs, I have downloaded the GTDB from the predefined database by the command mmseqs databases GTDB /my_path/GTDB tmp, then I run the command:

mmseqs taxonomy filter_contig_gclust_MMseqdb $GTDB_db/GTDB  filter_contig_gclust_GTDB_res tmp --threads 80 --remove-tmp-files
mmseqs createtsv filter_contig_gclust_MMseqdb  filter_contig_gclust_GTDB_res  filter_contig_gclust_GTDB_res.tsv

finally, I found there are some thing wrong, for the taxid and the taxon name cannot be found in the NCBI taxonomy database, and they are not match. here are part of the results:

k99_16878 1840 genus Faecalimonas 2 2 1 0.920 k99_25114_2 11880 species Anaerosporobacter mobilis 2 2 2 1.000 k99_30336_3 176 genus Clostridium 1 1 1 1.000 k99_11777_2 888 species Hafnia paralvei 1 1 1 1.000 k99_13149_3 11909 species Fournierella massiliensis 1 1 1 1.000 k99_53411_3 38757 species Faecalimonas sp900550975 2 2 1 0.950

I noticed the module Create a seqTaxDB for GTDB in the wiki page, I think maybe even though I downloaded the predefined database, I still need to do these process (build name.dmp, node.dmp from GTDB taxonomy), am I right?

If so, the problem is that the website https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ssu.fna isn't work, Can you help me ,please ?

[AnaMariaCabello]

Hi, I got the same problem. When I run the commands in [Create a seqTaxDB for GTDB] I got this error: mmseqs createdb ssu.fna ssu130.102.99.4 Connecting to data.ace.uq.edu.au (data.ace.uq.edu.au)|130.102.99.4|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2022-04-01 08:59:20 ERROR 404: Not Found. ... ... awk -F'\[loc' '{ print $1}' ssu.fna | awk "$buildNCBITax" awk: fatal: cannot open file `ssu.fna' for reading (No such file or directory)

Any help on this will be appreciated

[csm276]

Hi, I got the same problem. When I run the commands in [Create a seqTaxDB for GTDB] I got this error: mmseqs createdb ssu.fna ssu130.102.99.4 Connecting to data.ace.uq.edu.au (data.ace.uq.edu.au)|130.102.99.4|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2022-04-01 08:59:20 ERROR 404: Not Found. ... ... awk -F'[loc' '{ print $1}' ssu.fna | awk "$buildNCBITax" awk: fatal: cannot open file `ssu.fna' for reading (No such file or directory)

Any help on this will be appreciated

Hi， How did you resolve this issue at the time, until today I have also encountered this problem and this site is not working https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ssu.fna Can you give me some advice? Thanks a lot.

[AnaMariaCabello]

Hi,

I’m sorry but I can’t help. I couldn't use it at the end because of that problem. Best, Ana

On 3 Aug 2023, at 08:11, csm276 @. @.>> wrote:

Hi, I got the same problem. When I run the commands in [Create a seqTaxDB for GTDB] I got this error: mmseqs createdb ssu.fna ssu130.102.99.4 Connecting to data.ace.uq.edu.au http://data.ace.uq.edu.au/ (data.ace.uq.edu.au http://data.ace.uq.edu.au/)|130.102.99.4|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2022-04-01 08:59:20 ERROR 404: Not Found. ... ... awk -F'[loc' '{ print $1}' ssu.fna | awk "$buildNCBITax" awk: fatal: cannot open file `ssu.fna' for reading (No such file or directory)

Any help on this will be appreciated

Hi， How did you resolve this issue at the time, until today I have also encountered this problem and this site is not working https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ssu.fna https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ssu.fna Can you give me some advice? Thanks a lot.

— Reply to this email directly, view it on GitHub https://github.com/soedinglab/MMseqs2/issues/548#issuecomment-1663347073, or unsubscribe https://github.com/notifications/unsubscribe-auth/APMXFJCAL7ML33M3S4GNM33XTM6K3ANCNFSM5QJH4VIA. You are receiving this because you commented.

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Ana María Cabello Pérez, PhD

Centro Oceanográfico de Málaga (IEO-CSIC) Instituto Español de Oceanografía Puerto Pesquero s/n 29640 Fuengirola, Málaga, Spain Tel: +34 95 219 71 24 @.***

[csm276]

Hi Ana,

Thanks for your reply. Best, Ming

------------------ 原始邮件 ------------------ 发件人: "soedinglab/MMseqs2" @.>; 发送时间: 2023年8月3日(星期四) 晚上10:21 @.>; @.**@.>; 主题: Re: [soedinglab/MMseqs2] the website to download ssu.fna for GTDB doesn't work (Issue #548)

Hi,

I’m sorry but I can’t help. I couldn't use it at the end because of that problem. Best, Ana

> On 3 Aug 2023, at 08:11, csm276 @. @.>> wrote: >
>
> Hi, I got the same problem. When I run the commands in [Create a seqTaxDB for GTDB] I got this error: mmseqs createdb ssu.fna ssu130.102.99.4 Connecting to data.ace.uq.edu.au <http://data.ace.uq.edu.au/&gt; (data.ace.uq.edu.au <http://data.ace.uq.edu.au/&gt;)|130.102.99.4|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2022-04-01 08:59:20 ERROR 404: Not Found. ... ... awk -F'[loc' '{ print $1}' ssu.fna | awk "$buildNCBITax" awk: fatal: cannot open file `ssu.fna' for reading (No such file or directory) >
> Any help on this will be appreciated >
> Hi， > How did you resolve this issue at the time, until today I have also encountered this problem and this site is not working > https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ssu.fna <https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/ssu.fna&gt; > Can you give me some advice? Thanks a lot. >
> — > Reply to this email directly, view it on GitHub <https://github.com/soedinglab/MMseqs2/issues/548#issuecomment-1663347073&gt;, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APMXFJCAL7ML33M3S4GNM33XTM6K3ANCNFSM5QJH4VIA&gt;. > You are receiving this because you commented. >

---

Ana María Cabello Pérez, PhD

Centro Oceanográfico de Málaga (IEO-CSIC) Instituto Español de Oceanografía Puerto Pesquero s/n 29640 Fuengirola, Málaga, Spain
Tel: +34 95 219 71 24
@.***

---

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[sevengo8378]

find v89 of ssu.fna in GTDB history releases, url: https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/ssu_r89.fna

I run the commands in [Create a seqTaxDB for GTDB] and it works. Perhaps as a temporary alternative.