Aleksey Molokin

I'm also getting the no alias/index error when calling `diamond prepdb -d nr` on my newly downloaded nr db: > Error: NCBI C++ Exception: T0 "/root/ncbi-blast-2.11.0+-src/c++/src/objtools/blast/seqdb_reader/seqdbalias.cpp", line 320: Error: (CSeqDBException::eFileErr)...

Specify merged reads with --merged, unmerged reads with -s, and the original unmerged R1 and R2 reads with -1 and -2.

You would first interleave them into a single fastq file using tools such as seqtk, bbtools, etc.

After re-reading the documentation and a few related threads #751 #765 #891 the correct way actually appears to be: ``` --merged merged.fastq -1 R1_remaining_unmerged.fastq -2 R2_remaining_unmerged.fastq ``` Issue 751 initially...

> Hi, > > > > Thank you, however, I tried this. If you look at my first query and the log file you can see that I had provided...

I've also run into the issue of report files missing rank codes for root and domains. Just recently when using the [nt database](https://benlangmead.github.io/aws-indexes/k2) and also previously when using a custom...