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kensung-lab / hypo-assembler

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Compilation error #7

Open francicco opened 3 months ago

francicco commented 3 months ago

Hi,

During the compilation cmake returns me this error:

install -p -m 644 htslib/*.h /user/work/tk19812/software/hypo-assembler/overlap/libs/htslib-1.9/include/htslib
install -p -m 644 libhts.a /user/work/tk19812/software/hypo-assembler/overlap/libs/htslib-1.9/lib/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /user/work/tk19812/software/hypo-assembler/overlap/libs/htslib-1.9/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /user/work/tk19812/software/hypo-assembler/overlap/libs/htslib-1.9/share/man/man5
HTSlib installed.
CMake Error at CMakeLists.txt:33 (add_subdirectory):
  The source directory

    /user/work/tk19812/software/hypo-assembler/overlap/libs/sdsl-lite

  does not contain a CMakeLists.txt file.

-- Configuring incomplete, errors occurred!
See also "/user/work/tk19812/software/hypo-assembler/overlap/build/CMakeFiles/CMakeOutput.log".

Any help? Thanks a lot Francesco

joshua-casey commented 3 months ago

Hi Fransesco,

Seems like the submodules were not pulled. Did you run the clone the repository recursively? i.e.

git clone --recursive https://github.com/kensung-lab/hypo-assembler

I'll add the instruction to do the clone recursively in the readme.

Thank you. Sincerely, Joshua Casey Darian

francicco commented 3 months ago

Hi Joshua,

That fixed the problem. Now I'm running the demo you provided but I'm getting a bad_alloc error:

[STEP 5] Polishing
Error: std::bad_alloc
Input: ./hypo -d temp//overlap.fa -s 3G -B temp//overlap_long.bam -C 60 -b temp//overlap_short.bam -r @temp//shorts.txt -c 100 -t 40 -o temp//polished
[Hypo::Utils] Info: Value of K chosen for the given genome size (3G): 17
[Hypo::Utils] Info: File size expected for the given genome size (3G) and cov (100): 600G
Given Command: hypo  -d temp//overlap.fa -s 3G -B temp//overlap_long.bam -c 60 -b temp//overlap_short.bam -r @temp//shorts.txt -c 100 -t 40 -o temp//polished.
[Hypo::Utils] Info: Intermediate Files will NOT be stored.
[Hypo::Utils] Info: Beginning from stage: 0
RESOURCES ([SUK:KMC]: Running KMC done. ): TIME= 0.0957416 sec; PEAK RSS (so far)= 2073MB; CURRENT RSS (so far)= 2073MB.
Failed to open KMC database.
[Hypo::SolidKmers] Error: KMC Output: Could not have successful run of SUK for computing Solid kmers!

Not sure why Cheers F

joshua-casey commented 3 months ago

Hi Fransesco,

Sorry for the late reply - here the bad alloc seems to come when running KMC. You can try rerunning them now since there are some adjustments I made with default memory. If it's still not working, can you try running KMC independently on the input data?

i.e.

kmc -k17 @shorts.txt kmc_temp_dir/

Where shorts.txt just contains path to the two short reads files.

Thank you. Sincerely, Joshua Casey Darian