Closed aag1 closed 4 years ago
P.S. Please find attached full compilation log: metaviralSPAdes_compilation.log
If you wish to compile any of the SPAdes family tools including metaviralSPAdes you will need the following libraries to be pre-installed:
g++ (version 5.3.1 or higher) cmake (version 3.5 or higher) zlib libbz2
This error looks like you do not have zlib installed.
Dear Dmitry,
Thank you very much for pointing me to zlib! There was indeed a problem with it (apparently I had two versions, zlib 1.2.3 and zlib 1.2.11, loaded simultaneously), and after I fixed it compilation advanced beyond the point of previous error.
Unfortunately, after that the compilation failed with a new error message:
CMake Error at cmake_install.cmake:81 (file):
file INSTALL cannot find
"/PATH_TO_WORK_DIR/metaviralSPAdes/assembler/src/../manual.html".
make: *** [install] Error 1
Full compilation log: metaviralSPAdes_compilation2.log
Sorry for so many questions, but could you please advise if I can fix this new problem somehow?
Kind regards, Anastasia
Oops - this is my fault. Please revert to previous revision, (git revert HEAD) prior to compiling.
Thank you! I successfully reverted the last git commit.
Later, I faced a new problem: folders newly created during compilation were given wrong permissions on my server, resulting in compilation errors. I solved it by adding USE_SOURCE_PERMISSIONS
to every install(DIRECTORY
command in the following files:
assembler/src/CMakeLists.txt
assembler/src/projects/hammer/CMakeLists.txt
assembler/src/projects/ionhammer/CMakeLists.txt
assembler/src/projects/spades/CMakeLists.txt
assembler/src/spades_pipeline/CMakeLists.txt
After that, compilation run without error messages and bin/spades.py --test
passed correctly.
There was no metaviralspades.py
script or symlink in the bin/
, so I created a symlink myself (ln -s spades.py metaviralspades.py
). After that I was able to run bin/metaviralspades.py
for a sample. Resulting files contigs.fasta
and scaffolds.fasta
were identical and contained 62 entries. The file K127/before_chromosome_removal.fasta
contained 400,702 entries.
Could you please advise if my interpretation of the output is correct:
scaffolds.fasta
contains the potential complete viral genomesK127/before_chromosome_removal.fasta
contains all the assembled contigsKind regards, Anastasia
Sorry, my fault again, thank you for noticing. With latest commit fixed this and previous issue. (Actually there is no need in metaviralspades.py script in /bin folder - usually run it from ./assembler/metaviralspades.py but still, it should be copied there also)
scaffolds.fasta contains the potential complete viral genomes K127/before_chromosome_removal.fasta contains all the assembled contigs
Yes, it is correct. However there can be some false-positives in potential complete viral sequences - can suggest to check with either viralverify (https://github.com/ablab/viralVerify ) or with recently released checkV tool
Thank you very much!
Kind regards, Anastasia
Dear SPAdes team,
I am trying to install metaviralSPAdes using the following commands:
Compilation reaches 100%:
But fails with the following error message:
Could you please advise if I can fix it somehow?
Kind regards, Anastasia