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Santy-8128 / Minimac3

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
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make error - undefined references to "gz" objects #13

Open jerrywzy opened 4 years ago

jerrywzy commented 4 years ago

Hi there, I seem to have run into a problem with running make on the Minimac3 files. It gives an error as below: 

make[1]: Entering directory `reduser/programs/Minimac3/src'
make -C reduser/programs/Minimac3/Library/libStatGenForMinimac3 --no-print-directory opt
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o
g++  -std=c++0x -O4  -pipe -Wall -Wno-unknown-pragmas -Wno-unused-local-typedefs -Ireduser/programs/Minimac3/Library/libStatGenForMinimac3/include -I. -I ../  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Jun 27 17:36:13 +08 2020\"" -DUSER="\"lsiwzyj\""   -o ../bin/Minimac3     ../obj/HaplotypeSet.o ../obj/Unique.o ../obj/Imputation.o ../obj/MarkovModel.o ../obj/MarkovParameters.o ../obj/ImputationStatistics.o ../obj/Main.o      reduser/programs/Minimac3/Library/libStatGenForMinimac3/libStatGen.a     -lm -lz
reduser/programs/Minimac3/Library/libStatGenForMinimac3/libStatGen.a(GzipFileType.o): In function `GzipFileType::GzipFileType(char const*, char const*)':
GzipFileType.cpp:(.text+0xdf): undefined reference to `gzopen64'
reduser/programs/Minimac3/Library/libStatGenForMinimac3/libStatGen.a(GzipFileType.o): In function `GzipFileType::seek(long, int)':
GzipFileType.cpp:(.text._ZN12GzipFileType4seekEli[GzipFileType::seek(long, int)]+0x9): undefined reference to `gzseek64'
reduser/programs/Minimac3/Library/libStatGenForMinimac3/libStatGen.a(GzipFileType.o): In function `GzipFileType::tell()':
GzipFileType.cpp:(.text._ZN12GzipFileType4tellEv[GzipFileType::tell()]+0x5): undefined reference to `gztell64'
collect2: ld returned 1 exit status
make[1]: *** [../bin/Minimac3] Error 1
make[1]: Leaving directory `reduser/programs/Minimac3/src'
make: *** [src] Error 2

I have zlib 1.2.11 installed locally. I did also try to update glibc but that was unsuccessful and I am out of ideas at this point. Do you have any idea on this?

Thanks!