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aquaskyline / SOAP3-dp

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065632
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How to build from source #5

Closed anildadj closed 4 years ago

anildadj commented 4 years ago

Hi,

My system has 64GB of RAM and 4GB GDDR5 M1200 Nvidia GPU.

Please help resolve and run the program. I am trying to do "make" from inside the downloaded master folder.

But it gives error like -

SOAP3-DP.o: In functionmain': .SOAP3-DP.cpp:(.text.startup+0x1899): undefined reference to gzclose' .SOAP3-DP.cpp:(.text.startup+0x18b4): undefined reference togzclose' .SOAP3-DP.cpp:(.text.startup+0x22b5): undefined reference to gzopen' .SOAP3-DP.cpp:(.text.startup+0x22e0): undefined reference togzread' .SOAP3-DP.cpp:(.text.startup+0x2327): undefined reference to gzopen' .SOAP3-DP.cpp:(.text.startup+0x2352): undefined reference togzread' .SOAP3-DP.cpp:(.text.startup+0x2382): undefined reference to gzopen' .SOAP3-DP.cpp:(.text.startup+0x23b5): undefined reference togzread' .SOAP3-DP.cpp:(.text.startup+0x2418): undefined reference to gzopen' .SOAP3-DP.cpp:(.text.startup+0x2443): undefined reference togzread' .SOAP3-DP.cpp:(.text.startup+0x2658): undefined reference to gzeof' .SOAP3-DP.cpp:(.text.startup+0x2675): undefined reference togzerror' .SOAP3-DP.cpp:(.text.startup+0x28d5): undefined reference to gzeof' .SOAP3-DP.cpp:(.text.startup+0x28f2): undefined reference togzerror' QueryParser.o: In function loadPairReadsGz2(gzFile_s*, char*, gzFile_s*, char*, unsigned char*, unsigned int*, unsigned int*, unsigned int*, char*, char*, unsigned int, unsigned int, unsigned long&, char&, unsigned int&, unsigned long&, char&, unsigned int&, unsigned int, unsigned int, int, char&, int)': QueryParser.cpp:(.text+0x14a0): undefined reference togzread' QueryParser.cpp:(.text+0x15d2): undefined reference to gzread' QueryParser.cpp:(.text+0x175e): undefined reference togzeof' QueryParser.cpp:(.text+0x1776): undefined reference to gzeof' QueryParser.cpp:(.text+0x17ee): undefined reference togzerror' QueryParser.cpp:(.text+0x181e): undefined reference to gzread' QueryParser.cpp:(.text+0x1856): undefined reference togzread' QueryParser.cpp:(.text+0x186b): undefined reference to gzeof' QueryParser.cpp:(.text+0x18ce): undefined reference togzread' QueryParser.cpp:(.text+0x18fe): undefined reference to gzread' QueryParser.cpp:(.text+0x192e): undefined reference togzerror' QueryParser.cpp:(.text+0x1b1a): undefined reference to gzread' QueryParser.cpp:(.text+0x1b85): undefined reference togzread' QueryParser.cpp:(.text+0x1bb6): undefined reference to gzread' QueryParser.cpp:(.text+0x1bee): undefined reference togzread' QueryParser.cpp:(.text+0x1c26): undefined reference to gzread' QueryParser.o:QueryParser.cpp:(.text+0x1cce): more undefined references togzread' follow QueryParser.o: In function loadPairReadsGz2(gzFile_s*, char*, gzFile_s*, char*, unsigned char*, unsigned int*, unsigned int*, unsigned int*, char*, char*, unsigned int, unsigned int, unsigned long&, char&, unsigned int&, unsigned long&, char&, unsigned int&, unsigned int, unsigned int, int, char&, int)': QueryParser.cpp:(.text+0x1d19): undefined reference togzeof' QueryParser.cpp:(.text+0x1d33): undefined reference to gzerror' QueryParser.cpp:(.text+0x1d5e): undefined reference togzeof' QueryParser.cpp:(.text+0x1d7e): undefined reference to gzeof' QueryParser.cpp:(.text+0x1d9e): undefined reference togzeof' QueryParser.cpp:(.text+0x1db8): undefined reference to gzeof' QueryParser.cpp:(.text+0x1dd2): undefined reference togzerror' QueryParser.cpp:(.text+0x1df6): undefined reference to gzeof' QueryParser.cpp:(.text+0x1e10): undefined reference togzerror' QueryParser.cpp:(.text+0x1e36): undefined reference to gzeof' QueryParser.cpp:(.text+0x1e50): undefined reference togzerror' QueryParser.cpp:(.text+0x1e76): undefined reference to gzeof' QueryParser.cpp:(.text+0x1e90): undefined reference togzerror' QueryParser.cpp:(.text+0x1eb6): undefined reference to gzeof' QueryParser.cpp:(.text+0x1ee0): undefined reference togzread' QueryParser.cpp:(.text+0x1f1b): undefined reference to gzerror' QueryParser.cpp:(.text+0x1f3e): undefined reference togzeof' QueryParser.cpp:(.text+0x1f58): undefined reference to gzerror' QueryParser.cpp:(.text+0x1f86): undefined reference togzerror' QueryParser.cpp:(.text+0x1fae): undefined reference to gzerror' QueryParser.cpp:(.text+0x1fe3): undefined reference togzread' QueryParser.cpp:(.text+0x2188): undefined reference to gzread' QueryParser.cpp:(.text+0x22c6): undefined reference togzread' QueryParser.cpp:(.text+0x23fe): undefined reference to gzeof' QueryParser.cpp:(.text+0x241e): undefined reference togzeof' QueryParser.cpp:(.text+0x2496): undefined reference to gzerror' QueryParser.cpp:(.text+0x24be): undefined reference togzread' QueryParser.cpp:(.text+0x24f7): undefined reference to gzread' QueryParser.cpp:(.text+0x250d): undefined reference togzeof' QueryParser.cpp:(.text+0x256a): undefined reference to gzread' QueryParser.cpp:(.text+0x2582): undefined reference togzeof' QueryParser.cpp:(.text+0x2598): undefined reference to gzerror' QueryParser.cpp:(.text+0x25c6): undefined reference togzread' QueryParser.cpp:(.text+0x25fe): undefined reference to gzread' QueryParser.cpp:(.text+0x2636): undefined reference togzerror' QueryParser.cpp:(.text+0x2860): undefined reference to gzread' QueryParser.cpp:(.text+0x28d2): undefined reference togzread' QueryParser.cpp:(.text+0x2906): undefined reference to gzread' QueryParser.cpp:(.text+0x293e): undefined reference togzread' QueryParser.cpp:(.text+0x297e): undefined reference to gzread' QueryParser.o:QueryParser.cpp:(.text+0x29da): more undefined references togzread' follow QueryParser.o: In function loadPairReadsGz2(gzFile_s*, char*, gzFile_s*, char*, unsigned char*, unsigned int*, unsigned int*, unsigned int*, char*, char*, unsigned int, unsigned int, unsigned long&, char&, unsigned int&, unsigned long&, char&, unsigned int&, unsigned int, unsigned int, int, char&, int)': QueryParser.cpp:(.text+0x2a03): undefined reference togzeof' QueryParser.cpp:(.text+0x2a1e): undefined reference to gzeof' QueryParser.cpp:(.text+0x2a39): undefined reference togzeof' QueryParser.cpp:(.text+0x2a54): undefined reference to gzeof' QueryParser.cpp:(.text+0x2a6e): undefined reference togzerror' QueryParser.cpp:(.text+0x2a96): undefined reference to gzeof' QueryParser.cpp:(.text+0x2ab0): undefined reference togzerror' QueryParser.cpp:(.text+0x2ad6): undefined reference to gzeof' QueryParser.cpp:(.text+0x2af0): undefined reference togzerror' QueryParser.cpp:(.text+0x2b16): undefined reference to gzeof' QueryParser.cpp:(.text+0x2b30): undefined reference togzerror' QueryParser.cpp:(.text+0x2b66): undefined reference to gzread' QueryParser.cpp:(.text+0x2b9c): undefined reference togzeof' QueryParser.cpp:(.text+0x2bbf): undefined reference to gzerror' QueryParser.cpp:(.text+0x2bee): undefined reference togzread' QueryParser.cpp:(.text+0x2c3f): undefined reference to gzerror' QueryParser.cpp:(.text+0x2c6e): undefined reference togzerror' QueryParser.cpp:(.text+0x2c9e): undefined reference to gzerror' QueryParser.cpp:(.text+0x2cc6): undefined reference togzeof' QueryParser.cpp:(.text+0x2ce0): undefined reference to gzerror' QueryParser.cpp:(.text+0x2d0e): undefined reference togzerror' QueryParser.cpp:(.text+0x2d37): undefined reference to gzeof' QueryParser.cpp:(.text+0x2d59): undefined reference togzerror' QueryParser.cpp:(.text+0x2d86): undefined reference to gzeof' QueryParser.cpp:(.text+0x2da0): undefined reference togzerror' QueryParser.cpp:(.text+0x2dce): undefined reference to gzread' QueryParser.cpp:(.text+0x2e0a): undefined reference togzread' QueryParser.cpp:(.text+0x2e47): undefined reference to gzread' QueryParser.cpp:(.text+0x2e7d): undefined reference togzread' QueryParser.cpp:(.text+0x2eb0): undefined reference to gzeof' QueryParser.cpp:(.text+0x2edd): undefined reference togzeof' QueryParser.cpp:(.text+0x2eff): undefined reference to gzerror' QueryParser.cpp:(.text+0x2f56): undefined reference togzerror' QueryParser.cpp:(.text+0x2f76): undefined reference to gzeof' QueryParser.cpp:(.text+0x2f9d): undefined reference togzeof' QueryParser.cpp:(.text+0x2fb7): undefined reference to gzerror' QueryParser.cpp:(.text+0x2fd6): undefined reference togzeof' QueryParser.cpp:(.text+0x2ff0): undefined reference to gzerror' QueryParser.cpp:(.text+0x3023): undefined reference togzerror' QueryParser.cpp:(.text+0x3058): undefined reference to gzerror' QueryParser.cpp:(.text+0x3086): undefined reference togzeof' QueryParser.cpp:(.text+0x30a0): undefined reference to gzerror' QueryParser.o: In functionloadSingleReadsGz(gzFile_s, char, unsigned char, unsigned int, unsigned int, unsigned int, char, char, unsigned int, unsigned int, unsigned long&, char&, unsigned int&, unsigned int, unsigned int, int, char&, int)': QueryParser.cpp:(.text+0x32be): undefined reference to gzread' QueryParser.cpp:(.text+0x33f3): undefined reference togzread' QueryParser.cpp:(.text+0x3545): undefined reference to gzeof' QueryParser.cpp:(.text+0x3565): undefined reference togzeof' QueryParser.cpp:(.text+0x35e2): undefined reference to gzerror' QueryParser.cpp:(.text+0x360d): undefined reference togzread' QueryParser.cpp:(.text+0x3645): undefined reference to gzread' QueryParser.cpp:(.text+0x365b): undefined reference togzeof' QueryParser.cpp:(.text+0x36c5): undefined reference to gzread' QueryParser.cpp:(.text+0x36fd): undefined reference togzread' QueryParser.cpp:(.text+0x372a): undefined reference to gzerror' QueryParser.cpp:(.text+0x3904): undefined reference togzread' QueryParser.cpp:(.text+0x396c): undefined reference to gzread' QueryParser.cpp:(.text+0x399d): undefined reference togzread' QueryParser.cpp:(.text+0x39d5): undefined reference to gzread' QueryParser.cpp:(.text+0x3a0d): undefined reference togzread' QueryParser.o:QueryParser.cpp:(.text+0x3aad): more undefined references to gzread' follow QueryParser.o: In functionloadSingleReadsGz(gzFile_s, char, unsigned char, unsigned int, unsigned int, unsigned int, char, char, unsigned int, unsigned int, unsigned long&, char&, unsigned int&, unsigned int, unsigned int, int, char&, int)': QueryParser.cpp:(.text+0x3af8): undefined reference to gzeof' QueryParser.cpp:(.text+0x3b0e): undefined reference togzerror' QueryParser.cpp:(.text+0x3b35): undefined reference to gzeof' QueryParser.cpp:(.text+0x3b55): undefined reference togzeof' QueryParser.cpp:(.text+0x3b75): undefined reference to gzeof' QueryParser.cpp:(.text+0x3b8f): undefined reference togzeof' QueryParser.cpp:(.text+0x3ba5): undefined reference to gzerror' QueryParser.cpp:(.text+0x3bc5): undefined reference togzeof' QueryParser.cpp:(.text+0x3bdb): undefined reference to gzerror' QueryParser.cpp:(.text+0x3bfd): undefined reference togzeof' QueryParser.cpp:(.text+0x3c13): undefined reference to gzerror' QueryParser.cpp:(.text+0x3c35): undefined reference togzeof' QueryParser.cpp:(.text+0x3c4b): undefined reference to gzerror' QueryParser.cpp:(.text+0x3c6d): undefined reference togzeof' QueryParser.cpp:(.text+0x3c94): undefined reference to gzread' QueryParser.cpp:(.text+0x3cc9): undefined reference togzerror' QueryParser.cpp:(.text+0x3cf2): undefined reference to gzerror' QueryParser.cpp:(.text+0x3d15): undefined reference togzeof' QueryParser.cpp:(.text+0x3d2b): undefined reference to gzerror' QueryParser.cpp:(.text+0x3d52): undefined reference togzerror' QueryParser.cpp:(.text+0x3d7d): undefined reference to gzread' QueryParser.cpp:(.text+0x3da8): undefined reference togzerror' QueryParser.cpp:(.text+0x3dca): undefined reference to gzeof' QueryParser.cpp:(.text+0x3de5): undefined reference togzerror' QueryParser.cpp:(.text+0x3e05): undefined reference to gzeof' QueryParser.cpp:(.text+0x3e17): undefined reference togzerror' QueryParser.cpp:(.text+0x3e65): undefined reference to gzread' QueryParser.cpp:(.text+0x3e8c): undefined reference togzeof' QueryParser.cpp:(.text+0x3e9e): undefined reference to gzerror' samtools-0.1.18/bgzf.o: In functiondeflateblock(BGZF*, int)': bgzf.c:(.text+0xad): undefined reference to `deflateInit2' bgzf.c:(.text+0xc5): undefined reference to deflate' bgzf.c:(.text+0xda): undefined reference todeflateEnd' bgzf.c:(.text+0x152): undefined reference to deflateInit2_' bgzf.c:(.text+0x16b): undefined reference todeflate' bgzf.c:(.text+0x180): undefined reference to deflateEnd' bgzf.c:(.text+0x1d8): undefined reference todeflateInit2' bgzf.c:(.text+0x1f0): undefined reference to deflate' bgzf.c:(.text+0x205): undefined reference todeflateEnd' bgzf.c:(.text+0x27a): undefined reference to `deflateInit2' bgzf.c:(.text+0x28d): undefined reference to deflate' bgzf.c:(.text+0x29e): undefined reference todeflateEnd' bgzf.c:(.text+0x314): undefined reference to deflateEnd' bgzf.c:(.text+0x352): undefined reference tocrc32' bgzf.c:(.text+0x360): undefined reference to crc32' samtools-0.1.18/bgzf.o: In functionbgzf_readblock': bgzf.c:(.text+0xacc): undefined reference to `inflateInit2' bgzf.c:(.text+0xae1): undefined reference to inflate' bgzf.c:(.text+0xaf2): undefined reference toinflateEnd' bgzf.c:(.text+0x143a): undefined reference to inflateEnd' samtools-0.1.18/bgzf.o: In functionbgzfclose': bgzf.c:(.text+0x19bc): undefined reference to `deflateInit2' bgzf.c:(.text+0x19d3): undefined reference to deflate' bgzf.c:(.text+0x19e6): undefined reference todeflateEnd' bgzf.c:(.text+0x1b19): undefined reference to deflateEnd' bgzf.c:(.text+0x1b4e): undefined reference tocrc32' bgzf.c:(.text+0x1b5b): undefined reference to crc32' samtools-0.1.18/bam_import.o: In functionks_getuntil2(kstream_t, int, __kstring_t, int*, int) [clone .constprop.6]': bam_import.c:(.text+0x9b): undefined reference to gzread' samtools-0.1.18/bam_import.o: In functionbam_get_lines(char const, int)': bam_import.c:(.text+0x3aa): undefined reference to gzdopen' bam_import.c:(.text+0x47c): undefined reference togzread' bam_import.c:(.text+0x8ad): undefined reference to gzclose' bam_import.c:(.text+0x915): undefined reference togzopen' samtools-0.1.18/bam_import.o: In function sam_header_read2': bam_import.c:(.text+0x97f): undefined reference togzdopen' bam_import.c:(.text+0xa3a): undefined reference to gzread' bam_import.c:(.text+0xd3a): undefined reference togzread' bam_import.c:(.text+0x13a3): undefined reference to gzread' bam_import.c:(.text+0x1466): undefined reference togzclose' bam_import.c:(.text+0x195c): undefined reference to gzopen' samtools-0.1.18/bam_import.o: In functionsam_header_read': bam_import.c:(.text+0x209b): undefined reference to gzread' bam_import.c:(.text+0x23e6): undefined reference togzread' samtools-0.1.18/bam_import.o: In function sam_read1': bam_import.c:(.text+0x3238): undefined reference togzread' samtools-0.1.18/bam_import.o: In function sam_open': bam_import.c:(.text+0x4317): undefined reference togzdopen' bam_import.c:(.text+0x438b): undefined reference to gzopen' samtools-0.1.18/bam_import.o: In functionsam_close': bam_import.c:(.text+0x43cc): undefined reference to gzclose' samtools-0.1.18/razf.o: In functionrazf_openw(int)': razf.c:(.text+0x89): undefined reference to `deflateInit2' razf.c:(.text+0x116): undefined reference to deflateSetHeader' samtools-0.1.18/razf.o: In functionrazf_openr(int, int)': razf.c:(.text+0x62b): undefined reference to `inflateInit2' razf.c:(.text+0x6e5): undefined reference to inflateEnd' samtools-0.1.18/razf.o: In functionrazf_write': razf.c:(.text+0xcef): undefined reference to deflate' razf.c:(.text+0xf90): undefined reference todeflate' razf.c:(.text+0x12bf): undefined reference to deflate' razf.c:(.text+0x1381): undefined reference todeflate' samtools-0.1.18/razf.o: In function razf_read': razf.c:(.text+0x1a0d): undefined reference toinflate' samtools-0.1.18/razf.o: In function razf_skip(RandomAccessZFile*, int)': razf.c:(.text+0x1f74): undefined reference toinflate' samtools-0.1.18/razf.o: In function razf_jump(RandomAccessZFile*, long, int)': razf.c:(.text+0x21cc): undefined reference toinflateReset' samtools-0.1.18/razf.o: In function razf_seek': razf.c:(.text+0x23f4): undefined reference toinflateReset' samtools-0.1.18/razf.o: In function razf_seek2': razf.c:(.text+0x24b9): undefined reference toinflateReset' samtools-0.1.18/razf.o: In function razf_close': razf.c:(.text+0x263e): undefined reference toinflateEnd' razf.c:(.text+0x26a0): undefined reference to deflate' razf.c:(.text+0x26bd): undefined reference todeflateEnd' razf.c:(.text+0x28ed): undefined reference to deflate' collect2: error: ld returned 1 exit status Makefile:87: recipe for target 'SOAP3-DP' failed make: *** [SOAP3-DP] Error 1

aquaskyline commented 4 years ago

you should have libz installed.