Closed KseniaJuravel closed 3 months ago
jamorrison
commented
5 months ago Hi Ksenia,
Would you mind sending me what operating system you are working on?
One other quick thing to mention is if you don't have to build BISCUIT yourself, then you could try downloading one of the pre-compiled binaries (only works on x86 Macs or Linux systems) or installing via bioconda.
Best, Jacob
KseniaJuravel
commented
3 months ago Hi Jacob,
Thank you for answering, and I am sorry for the late reply.
I am using the following system: cat /etc/os-release PRETTY_NAME="CS HUJI debian 5782" ANSI_COLOR="1;34" NAME="Debian GNU/Linux" VERSION_ID="10" VERSION="10 (buster)" VERSION_CODENAME=buster ID=debian HOME_URL="https://www.debian.org/" SUPPORT_URL="https://www.debian.org/support" BUG_REPORT_URL="https://bugs.debian.org/"
As you suggested, I installed the last conda update, so it works fine.
Thank you, Ksenia
jamorrison
commented
3 months ago I'm glad to hear the latest conda update worked for you. Feel free to open another issue if you have further issues!
Hi all,
I am trying to install the tool using any of the options given (zip/git/compiled/source).
But I keep getting that:
$ sudo make && make install [ 1%] Creating directories for 'utils' [ 3%] Performing download step (git clone) for 'utils' Cloning into 'utils'... HEAD is now at 5f4aeab remove execute permissions [ 4%] Performing update step for 'utils' [ 6%] No patch step for 'utils' [ 7%] No configure step for 'utils' [ 9%] Performing build step for 'utils' [ 11%] No install step for 'utils' [ 12%] Completed 'utils' [ 12%] Built target utils [ 14%] Creating directories for 'sgsl' [ 15%] Performing download step (git clone) for 'sgsl' Cloning into 'sgsl'... HEAD is now at 6533277 ignore cmake generated dirs [ 17%] Performing update step for 'sgsl' [ 19%] No patch step for 'sgsl' [ 20%] No configure step for 'sgsl' [ 22%] Performing build step for 'sgsl' [ 23%] No install step for 'sgsl' [ 25%] Completed 'sgsl' [ 25%] Built target sgsl [ 26%] Creating directories for 'htslib' [ 28%] Performing download step for 'htslib' htslib-1.18.tar.bz2: OK [ 30%] No update step for 'htslib' [ 31%] No patch step for 'htslib' [ 33%] Performing configure step for 'htslib' checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk [ 34%] Performing build step for 'htslib' [ 36%] No install step for 'htslib' [ 38%] Completed 'htslib' [ 38%] Built target htslib [ 39%] Building C object lib/aln/CMakeFiles/aln_static.dir/QSufSort.c.o [ 41%] Building C object lib/aln/CMakeFiles/aln_static.dir/align.c.o [ 42%] Building C object lib/aln/CMakeFiles/aln_static.dir/bntseq.c.o [ 44%] Building C object lib/aln/CMakeFiles/aln_static.dir/bwa.c.o [ 46%] Building C object lib/aln/CMakeFiles/aln_static.dir/bwamem.c.o [ 47%] Building C object lib/aln/CMakeFiles/aln_static.dir/bwashm.c.o /home/Software/biscuit-1.4.0.20240108/lib/aln/bwashm.c: In function ‘bwa_shm_stage’: /home/Software/biscuit-1.4.0.20240108/lib/aln/bwashm.c:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] ftruncate(shmid, BWA_CTL_SIZE); ^
~~~~~~~~~ /home/Software/biscuit-1.4.0.20240108/lib/aln/bwashm.c:66:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] ftruncate(shmid, idx->l_mem); ^~~~~~~~ [ 49%] Building C object lib/aln/CMakeFiles/aln_static.dir/bwt.c.o [ 50%] Building C object lib/aln/CMakeFiles/aln_static.dir/bwt_gen.c.o [ 52%] Building C object lib/aln/CMakeFiles/aln_static.dir/bwtindex.c.o [ 53%] Building C object lib/aln/CMakeFiles/aln_static.dir/is.c.o [ 55%] Building C object lib/aln/CMakeFiles/aln_static.dir/kopen.c.o [ 57%] Building C object lib/aln/CMakeFiles/aln_static.dir/ksw.c.o [ 58%] Building C object lib/aln/CMakeFiles/aln_static.dir/kthread.c.o [ 60%] Building C object lib/aln/CMakeFiles/aln_static.dir/malloc_wrap.c.o [ 61%] Building C object lib/aln/CMakeFiles/aln_static.dir/mem_alnreg.c.o [ 63%] Building C object lib/aln/CMakeFiles/aln_static.dir/mem_alnreg_format.c.o [ 65%] Building C object lib/aln/CMakeFiles/aln_static.dir/mem_pair.c.o [ 66%] Building C object lib/aln/CMakeFiles/aln_static.dir/memchain.c.o [ 68%] Building C object lib/aln/CMakeFiles/aln_static.dir/smem_itr.c.o [ 69%] Building C object lib/aln/CMakeFiles/aln_static.dir/utils.c.o [ 71%] Linking C static library libaln.a [ 71%] Built target aln_static [ 73%] Building C object src/CMakeFiles/biscuit_core.dir/asm_pairwise.c.o [ 74%] Building C object src/CMakeFiles/biscuit_core.dir/bamfilter.c.o [ 76%] Building C object src/CMakeFiles/biscuit_core.dir/bc.c.o [ 77%] Building C object src/CMakeFiles/biscuit_core.dir/bisc_utils.c.o [ 79%] Building C object src/CMakeFiles/biscuit_core.dir/bsconv.c.o [ 80%] Building C object src/CMakeFiles/biscuit_core.dir/bsstrand.c.o [ 82%] Building C object src/CMakeFiles/biscuit_core.dir/cinread.c.o [ 84%] Building C object src/CMakeFiles/biscuit_core.dir/epiread.c.o [ 85%] Building C object src/CMakeFiles/biscuit_core.dir/epiread_rectangle.c.o [ 87%] Building C object src/CMakeFiles/biscuit_core.dir/main.c.o [ 88%] Building C object src/CMakeFiles/biscuit_core.dir/mergecg.c.o [ 90%] Building C object src/CMakeFiles/biscuit_core.dir/pileup.c.o [ 92%] Building C object src/CMakeFiles/biscuit_core.dir/qc.c.o [ 93%] Building C object src/CMakeFiles/biscuit_core.dir/tview.c.o [ 95%] Building C object src/CMakeFiles/biscuit_core.dir/vcf2bed.c.o [ 96%] Linking C static library libbiscuit_core.a [ 96%] Built target biscuit_core [ 98%] Building C object src/CMakeFiles/biscuit.dir/main.c.o [100%] Linking C executable biscuit /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(rANS_static4x16pr.o): In functionrans_enc_func': /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/rANS_static4x16pr.c:916: undefined reference topthread_once' /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/rANS_static4x16pr.c:916: undefined reference topthread_once' /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/rANS_static4x16pr.c:916: undefined reference topthread_once' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(rANS_static4x16pr.o): In functionrans_dec_func': /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/rANS_static4x16pr.c:971: undefined reference topthread_once' /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/rANS_static4x16pr.c:971: undefined reference topthread_once' libbiscuit_core.a(epiread.c.o): In functionmain_epiread': epiread.c:(.text+0x51e1): undefined reference topthread_create' epiread.c:(.text+0x5264): undefined reference topthread_create' epiread.c:(.text+0x54e8): undefined reference topthread_join' epiread.c:(.text+0x55c5): undefined reference topthread_join' libbiscuit_core.a(pileup.c.o): In functionmain_pileup': pileup.c:(.text+0x6e55): undefined reference topthread_create' pileup.c:(.text+0x6f6b): undefined reference topthread_create' pileup.c:(.text+0x71e8): undefined reference topthread_join' pileup.c:(.text+0x72c5): undefined reference topthread_join' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(sam.o): In functionsam_state_destroy': /home/Software/biscuit-1.4.0.20240108/lib/htslib/sam.c:3125: undefined reference topthread_join' /home/Software/biscuit-1.4.0.20240108/lib/htslib/sam.c:3125: undefined reference topthread_join' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(sam.o): In functionsam_read1_sam': /home/Software/biscuit-1.4.0.20240108/lib/htslib/sam.c:4062: undefined reference topthread_create' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(sam.o): In functionsam_write1': /home/Software/biscuit-1.4.0.20240108/lib/htslib/sam.c:4403: undefined reference topthread_create' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(thread_pool.o): In functionhts_tpool_init': /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:751: undefined reference topthread_mutexattr_init' /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:752: undefined reference topthread_mutexattr_settype' /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:754: undefined reference topthread_mutexattr_destroy' /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:765: undefined reference topthread_attr_getstacksize' /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:778: undefined reference topthread_create' /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:798: undefined reference topthread_join' /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:768: undefined reference topthread_attr_setstacksize' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(thread_pool.o): In functionhts_tpool_destroy': /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:1104: undefined reference topthread_join' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(thread_pool.o): In functionhts_tpool_kill': /home/Software/biscuit-1.4.0.20240108/lib/htslib/thread_pool.c:1130: undefined reference topthread_kill' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(utils.o): In functionhtscodecs_tls_alloc': /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/utils.c:122: undefined reference topthread_once' /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/utils.c:130: undefined reference topthread_getspecific' /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/utils.c:134: undefined reference topthread_setspecific' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(utils.o): In functionhtscodecs_tls_free': /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/utils.c:187: undefined reference topthread_getspecific' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(utils.o): In functionhtscodecs_tls_init': /home/Software/biscuit-1.4.0.20240108/lib/htslib/htscodecs/htscodecs/utils.c:104: undefined reference topthread_key_create' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(bgzf.o): In functionmt_destroy': /home/Software/biscuit-1.4.0.20240108/lib/htslib/bgzf.c:1815: undefined reference topthread_join' /home/Software/biscuit-1.4.0.20240108/lib/htslib/libhts.a(bgzf.o): In functionbgzf_thread_pool': /home/Software/biscuit-1.4.0.20240108/lib/htslib/bgzf.c:1760: undefined reference topthread_create' ../lib/aln/libaln.a(bwashm.c.o): In functionbwa_shm_test.part.0': bwashm.c:(.text+0x3a): undefined reference toshm_open' ../lib/aln/libaln.a(bwashm.c.o): In functionbwa_shm_stage': bwashm.c:(.text+0x139): undefined reference toshm_open' bwashm.c:(.text+0x245): undefined reference toshm_open' bwashm.c:(.text+0x3da): undefined reference toshm_open' bwashm.c:(.text+0x47d): undefined reference toshm_unlink' ../lib/aln/libaln.a(bwashm.c.o): In functionbwa_idx_load_from_shm': bwashm.c:(.text+0x50e): undefined reference toshm_open' bwashm.c:(.text+0x5b6): undefined reference toshm_open' ../lib/aln/libaln.a(bwashm.c.o): In functionbwa_shm_list': bwashm.c:(.text+0x676): undefined reference toshm_open' ../lib/aln/libaln.a(bwashm.c.o): In functionbwa_shm_destroy': bwashm.c:(.text+0x72e): undefined reference toshm_open' bwashm.c:(.text+0x799): undefined reference toshm_unlink' bwashm.c:(.text+0x7c6): undefined reference toshm_unlink' ../lib/aln/libaln.a(bwashm.c.o): In functionmain_shm': bwashm.c:(.text+0x905): undefined reference toshm_open' ../lib/aln/libaln.a(kthread.c.o): In functionkt_for': kthread.c:(.text+0x438): undefined reference topthread_create' kthread.c:(.text+0x452): undefined reference topthread_join' ../lib/aln/libaln.a(kthread.c.o): In functionkt_forpool_init': kthread.c:(.text+0x57e): undefined reference topthread_create' ../lib/aln/libaln.a(kthread.c.o): In functionkt_forpool_destroy': kthread.c:(.text+0x642): undefined reference topthread_join' ../lib/aln/libaln.a(kthread.c.o): In functionkt_pipeline': kthread.c:(.text+0x88e): undefined reference topthread_create' kthread.c:(.text+0x8ab): undefined reference topthread_join' collect2: error: ld returned 1 exit status src/CMakeFiles/biscuit.dir/build.make:104: recipe for target 'src/biscuit' failed make[2]: [src/biscuit] Error 1 CMakeFiles/Makefile2:254: recipe for target 'src/CMakeFiles/biscuit.dir/all' failed make[1]: [src/CMakeFiles/biscuit.dir/all] Error 2 Makefile:135: recipe for target 'all' failed make: *** [all] Error 2I have tried using the latest version and the older one.
I will be happy to receive any help or suggestions.
Thank you, Ksenia