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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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Output daa to STDOUT #332

Open jakewendt opened 4 years ago

jakewendt commented 4 years ago

I have a pipeline that I use to read fasta or bam files and pipe them through blastn and gzip and then up to AWS S3. It is literally a series of piped commands so as to avoid needing to figure out how much disk space I'd need on my AWS EC2 instance. Recently, I've been asked to use Diamond and to output the daa file format. However, when I use --outfmt 100, it creates the file .daa and doesn't pass anything through to STDOUT. I have tried using the --out /dev/stdout but this doesn't seem to work and errors with something like ...

Permission denied
Error: Error opening temporary file /dev/diamond-tmp-yqKhix

Is there a way that the daa output can be passed through STDOUT?

bbuchfink commented 4 years ago

It's not possible to write the DAA format to stdout, since this format is not being written linearly, but the program needs to seek within the file.

jakewendt commented 4 years ago

Thank you. I figured it was something like that.

Could notes be added to the documentation and perhaps check added on the out format and out filename and a warning message be displayed to avoid this silent "failure"?