The bioBakery help forum

Unable to use the WAALFE database

Hi there!

I’m trying to use WAAFLE to analyse metagenomes. I successfully downloaded all the package requirements for the software and downloaded the actual software. I also successfully downloaded the database and unzipped it. However, the syntax to USE the database (as printed below) did not produce the output file.

$ waafle_search contigs.fna waafledb/waafledb

When I cd’d into the waafledb directory, I found there was no single file named “waffledb” as listed above. Instead I found a series of files with file extensions .nhr, .nsq., and .nin. Was the database not configured correctly?

Thanks in advance,
Dottie

That all looks fine to me - what you are providing with the second argument (waafledb/waafledb) is the root name of the BLAST database files, i.e. the three files you named above. Did the command above produce any output to the screen (errors etc.)?

Here was the output, which is why I was wondering if maybe something wasn’t configuring properly:

(waafle_env) marisolortiz@Marisols-MacBook-Pro ISS % waafle_search F4_1S_S21_contigs.blastout /Users/marisolortiz/waafledb/waafledb

Executing command: blastn -query F4_1S_S21_contigs.blastout -db /Users/marisolortiz/waafledb/waafledb -out ./F4_1S_S21_contigs.blastout -max_target_seqs 10000 -num_threads 1 -outfmt ‘6 qseqid sseqid qlen slen length qstart qend sstart send pident positive gaps evalue bitscore sstrand’

BLAST Database error: No alias or index file found for nucleotide database [/Users/marisolortiz/waafledb/waafledb] in search path [/Users/marisolortiz/Desktop/ISS::]

Finished successfully.

Any thoughts? Thanks so much for replying!

Huh, that looks correct. To confirm, the individual database files live at…

/Users/marisolortiz/waafledb/waafledb.nhr

And so forth?

The other thing I noted is that your queries here are called F4_1S_S21_contigs.blastout, but I would expect them to be a FASTA file (like F4_1S_S21_contigs.fasta). I don’t think that’s the cause of this specific issue though.

That is where the files live! And I have tried using specific file names within that directory just to see if maybe something was missing from the tutorial. Any suggestions on what I might try? OR if I might be so bold and you have the time I could send you my email and we could briefly zoom about it? I could just be making some other mistake/maybe I didn’t download the dependencies appropriately?

With regards to the files I am using, I am trying to use a file of metagenomes. Is that not appropriate?

So many questions!

Dottie

I double-checked and the syntax you are using is correct - i.e. you want to provide the “root name” of the database files, of which there should be three. Is it possible that the database files didn’t download/unpack correctly?

The input to the first step of WAAFLE should be a FASTA file containing metagenomic contigs. You can compare your input file with the demo input file to make sure it is formatted similarly.

Hi @franzosa
I have the same issue while using waafle. The database if downloaded and all 16 files waafledb.00.nhr,.nin, .nsq and same for 02,03,04 and waafledb.nal are present at /data/databases/waffle/waafledb. Similarly a .tar file and tsv file are present in the waffle folder mentioned here.

I tried using the following command from my working directory where the contig file is present:
waafle_search Run1_S2.contigs.fa /data/databases/waffle/waafledb

It ends up with the same error:
Executing command: blastn -query Run1_S1.contigs_shortheader.fa -db /data/databases/waffle/waafledb -out ./Run1_S1.blastout -max_target_seqs 10000 -num_threads 1 -outfmt ‘6 qseqid sseqid qlen slen length qstart qend sstart send pident positive gaps evalue bitscore sstrand’
BLAST Database error: No alias or index file found for nucleotide database [/data/databases/waffle/waafledb] in search path [/working/dir/path/waafle::]
Finished successfully.

Any help would be appreciated.

Thank you
DP

If all of the waafledb files live in the following folder:

/data/databases/waffle/waafledb

Then the command you want is:

waafle_search Run1_S2.contigs.fa /data/databases/waffle/waafledb/waafledb

Noting the additional waafledb at the end of the above path. You are trying to point BLAST at the “basename” of all the database files (i.e. the name minus any file extensions), rather than the folder that contains those files. Sorry for the confusion!

@franzosa
Thank you very much, it worked well this way.
Thank you
DP