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Griffan / VerifyBamID

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
http://griffan.github.io/VerifyBamID/
92 stars 15 forks source link

error #21

Closed Myskiper closed 4 years ago

Myskiper commented 4 years ago

i git clone and cmake -DHTS_INCLUDE_DIRS=/envs/htslib/include/ -DHTS_LIBRARIES=/envs/htslib/lib/libhts.a .. after make, I got this: Scanning dependencies of target statgen [ 1%] Building CXX object statgen/CMakeFiles/statgen.dir/BaseAsciiMap.cpp.o [ 3%] Building CXX object statgen/CMakeFiles/statgen.dir/BaseUtilities.cpp.o [ 5%] Building CXX object statgen/CMakeFiles/statgen.dir/BgzfFileType.cpp.o [ 7%] Building CXX object statgen/CMakeFiles/statgen.dir/BgzfFileTypeRecovery.cpp.o [ 8%] Building CXX object statgen/CMakeFiles/statgen.dir/CharBuffer.cpp.o [ 10%] Building CXX object statgen/CMakeFiles/statgen.dir/Cigar.cpp.o [ 12%] Building CXX object statgen/CMakeFiles/statgen.dir/CigarRoller.cpp.o [ 14%] Building CXX object statgen/CMakeFiles/statgen.dir/Error.cpp.o [ 15%] Building CXX object statgen/CMakeFiles/statgen.dir/ErrorHandler.cpp.o [ 17%] Building CXX object statgen/CMakeFiles/statgen.dir/FileType.cpp.o [ 19%] Building CXX object statgen/CMakeFiles/statgen.dir/Generic.cpp.o [ 21%] Building CXX object statgen/CMakeFiles/statgen.dir/GenomeSequence.cpp.o [ 22%] Building CXX object statgen/CMakeFiles/statgen.dir/GzipFileType.cpp.o [ 24%] Building CXX object statgen/CMakeFiles/statgen.dir/GzipHeader.cpp.o [ 26%] Building CXX object statgen/CMakeFiles/statgen.dir/Hash.cpp.o [ 28%] Building CXX object statgen/CMakeFiles/statgen.dir/IndexBase.cpp.o [ 29%] Building CXX object statgen/CMakeFiles/statgen.dir/InputFile.cpp.o [ 31%] Building CXX object statgen/CMakeFiles/statgen.dir/IntArray.cpp.o [ 33%] Building CXX object statgen/CMakeFiles/statgen.dir/MathMatrix.cpp.o [ 35%] Building CXX object statgen/CMakeFiles/statgen.dir/MathVector.cpp.o [ 36%] Building CXX object statgen/CMakeFiles/statgen.dir/MemoryMap.cpp.o [ 38%] Building CXX object statgen/CMakeFiles/statgen.dir/MemoryMapArray.cpp.o [ 40%] Building CXX object statgen/CMakeFiles/statgen.dir/PhoneHome.cpp.o [ 42%] Building CXX object statgen/CMakeFiles/statgen.dir/STLUtilities.cpp.o [ 43%] Building CXX object statgen/CMakeFiles/statgen.dir/Sort.cpp.o [ 45%] Building CXX object statgen/CMakeFiles/statgen.dir/StatGenStatus.cpp.o [ 47%] Building CXX object statgen/CMakeFiles/statgen.dir/StringArray.cpp.o [ 49%] Building CXX object statgen/CMakeFiles/statgen.dir/StringBasics.cpp.o [ 50%] Building CXX object statgen/CMakeFiles/statgen.dir/StringHash.cpp.o [ 52%] Building CXX object statgen/CMakeFiles/statgen.dir/Tabix.cpp.o [ 54%] Building CXX object statgen/CMakeFiles/statgen.dir/UncompressedFileType.cpp.o [ 56%] Building C object statgen/CMakeFiles/statgen.dir/knetfile.c.o [ 57%] Linking CXX static library libstatgen.a [ 57%] Built target statgen Scanning dependencies of target Vcf [ 59%] Building CXX object libVcf/CMakeFiles/Vcf.dir/libVcfVcfFile.cpp.o [ 61%] Linking CXX static library libVcf.a [ 61%] Built target Vcf Scanning dependencies of target samtools [ 63%] Building C object samtools/CMakeFiles/samtools.dir/bam.c.o [ 64%] Building C object samtools/CMakeFiles/samtools.dir/bam_aux.c.o [ 66%] Building C object samtools/CMakeFiles/samtools.dir/bam_index.c.o [ 68%] Building C object samtools/CMakeFiles/samtools.dir/bam_mate.c.o [ 70%] Building C object samtools/CMakeFiles/samtools.dir/bam_md.c.o [ 71%] Building C object samtools/CMakeFiles/samtools.dir/bam_sort.c.o [ 73%] Building C object samtools/CMakeFiles/samtools.dir/bam_stat.c.o [ 75%] Building C object samtools/CMakeFiles/samtools.dir/bamtk.c.o [ 77%] Building C object samtools/CMakeFiles/samtools.dir/bedidx.c.o [ 78%] Building C object samtools/CMakeFiles/samtools.dir/kprobaln.c.o [ 80%] Building C object samtools/CMakeFiles/samtools.dir/sam_opts.c.o [ 82%] Building C object samtools/CMakeFiles/samtools.dir/sample.c.o [ 84%] Linking C static library libsamtools.a [ 84%] Built target samtools Scanning dependencies of target VerifyBamID [ 85%] Building CXX object CMakeFiles/VerifyBamID.dir/main.cpp.o [ 87%] Building CXX object CMakeFiles/VerifyBamID.dir/SVDcalculator.cpp.o [ 89%] Building CXX object CMakeFiles/VerifyBamID.dir/ContaminationEstimator.cpp.o [ 91%] Building CXX object CMakeFiles/VerifyBamID.dir/MathGenMin.cpp.o [ 92%] Building CXX object CMakeFiles/VerifyBamID.dir/MathGold.cpp.o [ 94%] Building CXX object CMakeFiles/VerifyBamID.dir/Random.cpp.o [ 96%] Building CXX object CMakeFiles/VerifyBamID.dir/SimplePileupViewer.cpp.o [ 98%] Building CXX object CMakeFiles/VerifyBamID.dir/params.cpp.o [100%] Linking CXX executable ../bin/VerifyBamID /usr/bin/ld: BFD version 2.20.51.0.2-5.47.el6_9.1 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size

/usr/bin/ld: Please report this bug.

collect2: 错误：ld 返回 1 make[2]: [../bin/VerifyBamID] 错误 1 make[2]: 正在删除文件“../bin/VerifyBamID” make[1]: [CMakeFiles/VerifyBamID.dir/all] 错误 2 make: [all] 错误 2

i also try to install from conda (https://anaconda.org/bioconda/verifybamid2), but i always met this error: /envs/VerifyBamID2/bin/verifybamid2 --RefVCF ReferencePanel.vcf.gz --Reference ./resource/test/chr20.fa.gz VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

Version:1.0.6 Copyright (c) 2009-2018 by Hyun Min Kang and Fan Zhang This project is licensed under the terms of the MIT license.

The following parameters are available. Ones with "[]" are in effect:

Available Options Input/Output Files : --BamFile [Empty], --PileupFile [Empty], --Reference [Empty], --SVDPrefix [/envs/VerifyBamID2/share/verifybamid2-1.0.6-2/resource/--RefVCF.ReferencePanel.vcf.gz.--Reference.vcf.gz.dat], --Output [result] Model Selection Options : --WithinAncestry, --DisableSanityCheck, --NumPC [2], --FixPC [Empty], --FixAlpha [-1.0e+00], --KnownAF [Empty], --NumThread [4], --Seed [12345], --Epsilon [1.0e-08], --OutputPileup, --Verbose Construction of SVD Auxiliary Files : --RefVCF [Empty] Deprecated Options : --UDPath [Empty], --MeanPath [Empty], --BedPath [Empty]

Cannot correspond command line parameter ./resource/test/chr20.fa.gz (#3) to any of the options

FATAL ERROR - Problems encountered parsing command line:

Cannot correspond command line parameter ./resource/test/chr20.fa.gz (#3) to any of the options

Exiting due to ERROR: Exception was thrown

Griffan commented 4 years ago

Thanks for the feedback. The first issue seems to be related to ld, the solution could be to upgrade ld or install binutil using conda.

The second issue is true. I will try to fix it. But I think this bug only relates to building customized resource files, if you just need estimation, you should still be able to use it.

Myskiper commented 4 years ago

Thank you for your quickly reply! Cause I get some bams which aligned to UCSC hg19, I try to generate resource files from our reference genome.

Griffan commented 4 years ago

@Myskiper I think now the recipe has been updated and synced, you should be able to use --RefVCF option directly now. Please let me know otherwise. Note that you may need to add conda-forge channel into the installing cmdline:

conda install -c bioconda -c conda-forge verifybamid2
Myskiper commented 4 years ago

thank you! i reinstall and it work fine! And i test some bam file, But I met warn: Insufficient Available markers, check input bam depth distribution in output pileup file after specifying --OutputPileup

Dose this mean VerifyBamID can't check this kind of bam Because it interrupt. I test five bam, and met two.

Griffan commented 4 years ago

This only means that your bam files have very few overlapping markers with your resource files. You can either disable sanity check( with --DisableSanityCheck) or prepare you customized resource files in restricted regions where the sequences are captured from.

Myskiper commented 4 years ago

Thank you very much! I'll try it!