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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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LCA_tax/taxid.db not present #691

Closed lilyyycao closed 12 months ago

lilyyycao commented 1 year ago

Hello,

I am trying to download the databases using the download_databases.pl command and come across the following error:

WARNING: Some SqueezeMeta dependencies could not be found in your environment! The LCA_tax/taxid.db database is not present in /gpfs/scratch/lyc5319/SqueezeMetaDatabase/db, it is malformed, or there is other problem with your SQLite configuration

I found a few issues bringing up similar errors but was not sure if there was solution to download this missing database.

This is so far what has been downloaded in my db folder.

image

Thank you!

fpusan commented 1 year ago

It seems that either the download or the decompression did not complete successfully. Do you have enough free disk space? If so, you can try redownloading.

lilyyycao commented 1 year ago

Hello, thank you for your response. I had tried downloading via all 3 methods listed (download, make, and make.alt) but still have consistently run across the same error. All of my files are being saved onto a cluster server and should have plenty of disk space, but it seems to consistently have errors here. I am running this on UBUNTU 22.04.2 and I am mainly looking to take some assemblies I had previously made and use SqueezeMeta to annotate them against the pfam, nr, and kegg databases. I also want to ask if the other files in my db folder look are look fully downloaded and configured and it is just the this one that is an issue. Thank you

fpusan commented 1 year ago

Hi! That is unfortunate, I am now trying to download the databases myself to see if I run into the same error. Meanwhile can you download directly from here? http://andes.cnb.csic.es/SqueezeMeta/SqueezeMetaDB.md5 http://andes.cnb.csic.es/SqueezeMeta/SqueezeMetaDB.tar.gz The md5sum of SqueezeMetaDB.tar.gz should be the same as stated in the SqueezeMetaDB.md5 file. If this works for you then uncompress the SqueezeMetaDB.tar.gz file. You should get a directory named db. Then you can call configure_nodb.pl /path/to/db and it should set things up for you.

fpusan commented 1 year ago

Hi again. Just confirming that I managed to successfully run download_databases.pl from my workstation in Sweden and it still works ok, so the problem may be related to your conexion/system. Let me know whether the manual download works