huangs001
commented
2 years ago Hi.
The problem is about the compiling of mecat. Check if the “XXX/AlignGraph2/thirdparty/mecat” exists or has content in it. If it doesn't exist or no content, need to initialize the submodule by git submodule init and git submodule update or by git clone --recursive XXX when git clone. There are two submodules "AlignGraph2/thirdparty/mecat" and "AlignGraph2/mecat_plus".
If it doesn't make sense, you can try to download MECAT separately and compiling, then move or copy the files into “XXX/AlignGraph2/thirdparty/mecat”.
It is a very interesting pipeline that I want to use it to help me assemble the genome. But while I am trying to install with " python3.9 install.py". """ Building with 4 threads Number of threads can be modified by adding '-t {thread_num}' Log file is located in ~/AlignGraph2/build.log Building PAGraph... Done. Took 2.081 seconds Building MECAT... Failed to build mecat2ref, please check XXX/AlignGraph2/build.log """
and the log file is """ Begin of Building PAGraph Being of CMake -- Configuring done -- Generating done -- Build files have been written to: XXX/AlignGraph2/PAGraph/build End of CMake Begin of make Consolidate compiler generated dependencies of target kmer_counter [ 25%] Built target kmer_counter Consolidate compiler generated dependencies of target pa_cns Consolidate compiler generated dependencies of target pre_process Consolidate compiler generated dependencies of target pagraph [ 50%] Built target pa_cns [ 86%] Built target pre_process [100%] Built target pagraph End of make End of Building PAGraph Begin of Building MECAT+ Begin of make make: *** No targets specified and no makefile found. Stop. """ All the requirements has been installed. I dont know how to fix it, can you help me?