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affinis / SMTa

Spatial meta-transcriptome analysis pipeline
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how to download the correct nt database #2

Open youwh1996 opened 1 year ago

youwh1996 commented 1 year ago
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I downloaded this files, but when I run test files, BLAST Database error: No alias or index file found for nucleotide database

affinis commented 1 year ago

I think you have correctly downloaded the nt database, just decompress these files with the suffix '.gz' with command tar -zxvf in that folder.

youwh1996 commented 1 year ago

I decompressed these files but still reported BLAST Database error: No alias or index file found for nucleotide database

affinis commented 1 year ago

could you please show files under that folder after decompression? and show your src/configs.conf file here, and make sure you have run "install_SMTa.sh".

youwh1996 commented 1 year ago
image image
affinis commented 1 year ago

图片 I don't know if files under your database folder is complete as you did not show them all, this is files under our folder, please check, if everything is ok, check database path in configs.conf, for example, if files like "nt.00.nin ..." is under “/home/youwh/reference/database/”, just specify "/home/youwh/reference/database/nt" instead of "/home/youwh/reference/database/nt/nt", unless you have created a folder named "nt" for these files. The other possible reason for this bug is the version of blast+, I remember sometimes blast database is version dependent, it may occur in some version due to the update of databse structure, so you could try to install other versions of blast+.

StackChan commented 3 months ago

For me it's bash install_SMTa.sh -n /data/pub/tools/nt/nt -b /data/pub/tools/ncbi-blast-2.15.0+/bin/blastn -s /data/pub/tools/spaceranger-2.0.0/spaceranger

I have nt database under /data/pub/songkang/nt/ as follows, ├── nt.126.nhr ├── nt.126.nin ├── nt.126.nsq ├── nt.127.nhr ├── nt.127.nin ├── nt.127.nsq ├── nt.fa

So why do i use /data/pub/tools/nt/nt? Please refer to blog

And if I use /data/pub/tools/nt, I encouter the problem just same as you, BLAST Database error: No alias or index file found for nucleotide database.

When I use /data/pub/tools/nt/nt, the result of ./run_SMTa_test.sh is `Waiting 6 seconds for UI to do final refresh. Pipestance completed successfully!

2024-07-09 07:01:17 Shutting down. Saving pipestance info to "tinytest/tinytest.mri.tgz" Warning: [blastn] Examining 5 or more matches is recommended`

So I guess it works.