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makedb progenomes fails #273
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update kaiju to the latest version from GitHub. The URL for the progenomes download changed since release v1.9.2. I should make a new release including this fix.. |
Thanks, done. 96Gb RAM, Debian GNU/Linux 11 (bullseye) |
Have a look at the table in the README for the memory requirements for building the kaiju index for each available reference database. For proGenomes v3 it is 120GB of RAM. |
I would like to install the latest version because of the same issue , but unfortunately the conda version I downloaded is still recording v1.9.2 despite bioconda page saying its 1.10.0 and the
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Just tried to install v1.10.0 via conda and got the correct version. You can also just compile it from source and run it without need for root. |
I have encountered the same problem: \033[0;32mExtracting taxdump.tar.gz\033[0m infilename= refseq/kaiju_db_refseq.faaoutfilename= refseq/kaiju_db_refseqAlphabet= ACDEFGHIKLMNPQRSTVWYnThreads= 10length= 0.000000checkpoint= 3caseSens=OFFrevComp=OFFterm= *revsort=OFFhelp=OFFSequences read time = 339.643674s Is this the problem with RAM? |
Probably. See the README for required RAM for each reference database. You can also download premade indexes. |
but the indexes offered on kaiju website is a little outdatetd, is there a way to locally make the index with out this much RAM? the server i work on has about 115gb of free RAM, just short to build the current refseq index |
You won't loose much when using the index file from last year. The memory requirements cannot be reduced.. |
Hello!
I'm trying to download progenomes database and see that:
Downloading taxdump.tar.gz
.listing [ <=> ] 1.85K --.-KB/s in 0.01s
2023-11-23 13:11:56 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz [1890] -> ".listing" [1]
taxdump.tar.gz 100%[=========================================================================>] 60.88M 13.6MB/s in 5.5s
2023-11-23 13:12:03 URL: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz [63835104] -> "taxdump.tar.gz" [1]
Extracting taxdump.tar.gz
Downloading proGenomes database
https://progenomes.embl.de/data/repGenomes/freeze12.proteins.representatives.fasta.gz:
2023-11-23 13:12:16 ERROR 404: Not Found.
What should I do?
Thanks.
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