DIAMOND v2.0.11

[bbuchfink]

• Fixed a bug that could cause invalid output when using --masking 0 combined with the global ranking mode.
• Enabled lazy repeat masking in the query-indexed and contiguous seed modes when using global ranking.
• Added detection of cache size to auto-enable query-indexed mode.

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This discussion was created from the release DIAMOND v2.0.11.

[FredericBGA]

Hello

I've compiled this version (as well as the 2.0.10) from sources.
The prepdb command is not included?

#diamond version
diamond version 2.0.11
#diamond prepdb -d Tmp/Rice.fasta
Error: Invalid command: prepdb. To print help message: diamond help

Do I need to add something during the compilation process?

[bbuchfink]

prepdb is only for using BLAST databases, so you need to compile with BLAST database support if you want to use that, which is pretty elaborate (see installation in the wiki).

[FredericBGA]

sorry, I've missed the wiki dedicated to this specific installation.

I've compiled Blast again with the recommended options.

[root@universe build#]ls /softs/biotools/diamond-blast-2.12.0/lib/libseqdb
libseqdb-static.a libseqdb.a

But the libs are not found, I will try to understand why now.

[root@universe build#]cmake -DBLAST_INCLUDE_DIR=/softs/biotools/diamond-blast-2.12.0/include/ncbi-tools++ -DBLAST_LIBRARY_DIR==/softs/biotools/diamond-blast-2.12.0/lib ..
-- The C compiler identification is GNU 6.2.0
-- The CXX compiler identification is GNU 6.2.0
-- Check for working C compiler: /softs/gcc/6.2.0/bin/gcc
-- Check for working C compiler: /softs/gcc/6.2.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /softs/gcc/6.2.0/bin/c++
-- Check for working CXX compiler: /softs/gcc/6.2.0/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Performing Test HAS_GNUPP14
-- Performing Test HAS_GNUPP14 - Success
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
BLAST_INCLUDE_DIR: /softs/biotools/diamond-blast-2.12.0/include/ncbi-tools++
BLAST_LIBRARY_DIR: =/softs/biotools/diamond-blast-2.12.0/lib
CMake Error at CMakeLists.txt:297 (message):
Unable to find BLAST library: seqdb

[bbuchfink]

Don't use two = here: -DBLAST_LIBRARY_DIR==

[FredericBGA]

rhoo, shame on me! thank you...