Diamond v.2.1.6 not recognizing input .fasta files

[BirdmanRidesAgain]

Hi, I'm trying to run Diamond v.2.1.6, installed via the bioconda distribution, on a set of fasta files, using the following code:

diamond blastx --query HOU_ASM.purged.fa \
--db /path/to/reference_proteomes/ \
outfmt 6 qseqid staxids bitscore qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore \
--sensitive \
--max-target-seqs 1 \
--evalue 1e-25 \
--threads 10 > Tridacna_squamosina_flye_racon.diamond.blastx.out

However, every input fasta I've tried returns the same error:

Error: Error detecting input file format. First line must begin with '>' (FASTA) or '@' (FASTQ)

The fasta work in blastn, but I can't seem to get them to run here, and running head confirms that they do begin with a '>'. I tried running dos2unix on them, on the off chance that there were some newlines or something interfering, but that didn't work. Any guidance you have would be appreciated.

[bbuchfink]

I can't reproduce the problem. If you send me the query file in question I can look further.

[BirdmanRidesAgain]

Of course. I’ve subsampled the fasta to one to decrease the size enough to send via email, but it does still reproduce the error on my end. However, if you can’t reproduce it, I assume there might be something wrong with the installation and/or distribution on my end. I’ll try and reinstall via bioconda to see if that sorts it out. 

On May 30, 2023, at 1:53 PM, Benjamin Buchfink @.***> wrote:

I can't reproduce the problem. If you send me the query file in question I can look further.

— Reply to this email directly, view it on GitHub https://github.com/bbuchfink/diamond/issues/705#issuecomment-1568219746, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATYEVUIRSU2WSUIKGWCLN4DXIXGSVANCNFSM6AAAAAAYNG542E. You are receiving this because you authored the thread.

[LR-2021]

Hi, I am getting the same issue. I have tested several versions. Have you solved the problem?

Thanks

[bbuchfink]

Hi, I am getting the same issue. I have tested several versions. Have you solved the problem?

Thanks

What is your operating system and how did you download diamond? Can you send me your query file?

[NantiaL]

Hey, same happens in version 2.0.11. I will send you my query file.

[LR-2021]

Hi,

I haven't answered yet because it seems I have solved the problem. However, I'm still waiting to check the blastx results, which have been pending for the last 4 days. There was another issue, #726, which might have been related, but I cannot confirm it completely yet.

Following @bbuchfink's suggestion, I tested diamond with test data, and it worked perfectly. Then, I checked the headers (see #726) and confirmed that @bbuchfink was correct; I was somehow missing the correct header line in the -taxonmap file.

After that, I ran diamond without any problems, but I am still waiting for the results. Hopefully, it worked.