Benjamin Buchfink
Benjamin Buchfink
Looks like there is a problem with `--target-indexed`. It will be fixed. What's your reason for using it? It was made for very particular applications only.
It should be fixed in the latest release. The index format has never been changed.
The memory use can be expected to be roughly 18*b/c + 2*b (in gigabytes). With enough memory it is first recommended to use c=1 and then increase the block size....
There seems to be an incompatibility between frameshift alignment mode and `--iterate`. I will look into fixing this, for now you need to run without `--iterate`.
`-g N` enables global ranking which means only the best N targets will be extended for each query, ranked on their ungapped extension score. This can be much faster than...
I don't know why it would take longer with more threads. I would have to investigate further, ideally using your data. Also not sure about your hardware setup. Does you...
Try to use the option `--no-unlink`.
No idea but you need not worry, that option does not change the results.
Looks like an error in the NCBI code, that has been fixed now. I managed to compile it using this procedure: https://github.com/bbuchfink/diamond/blob/master/Dockerfile
I got the same error compiling BLAST 2.16 itself using GCC 15. It needs to be fixed by NCBI, or you can use the ncbi-toolkit method.