biocodz
error in the help string. 10,000 is the default.
This is a good question and very neatly asked at that. I wish to be able to answer it just as neat, but no luck I'm afraid. The E-value concept...
Yeah, it's a weak spot. Many users use archived files as the input, and efficient mutlithreaded splitting of the archives is Hard to implement. Whence the splitting becomes a bottleneck...
Your guess seems to be correct.
It's not possible to say what's wrong from the info provided. I would start with running the command without the container first to get a handle on the program behaviour....
Yeah, that's a weak part of the project still waiting for improvement.
`-ref` takes a path to the reference file. ``` sortmerna -h --ref PATH Required Reference file (FASTA) absolute or relative path. Use multliple times, once per a reference file ```...
You can optionally specify the index directory location ``` --idx-dir PATH Optional Directory for storing Reference index. WORKDIR/idx ``` Overall the indexing has changed a bit since v2.1 (along with...
What version of sortmerna do you use?
I'm looking at the results of the [test 18](https://github.com/biocore/sortmerna/blob/master/scripts/test.jinja#L1259) (just randomly picked and ran on my laptop). Here are a few random records from the blast report: ``` DRR121111.1.1 EU602318...