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  • Install dwgsim problem - location of samtools binaries error

    Hi,

    I have attempted (so far unsucessfully) to install dwgsim.
    The installation notes suggests that there is a dependancy on the presence of samtools.
    I have samtools v 0.1.18 installed to usr/local/bin

    the install instructions for dwgsim:

    === Prerequisites ======= SAMtools ====SAMtools version >=0.1.7 is required. Please find SAMtoolsat http://samtools.sourceforge.net
    Download the source code and place it in the root directory. After, execute the following commands:
    tar -zxvf samtools-0.1.7.tar.gz
    ln -s samtools-0.1.7 samtools

    === Building DWGSIM ===To build DWGSIM, execute the following commands: make

    To install DWGSIM, after building, copy the following binariesto their appropriate installation directories:
    dwgsim
    dwgsim_eval
    dwgims_pileup_eval.pl

    I already have samtools installed. I understand from the above that that dwgsim needs the samtools binaries to install. I cant figure out however where to put them relative to the folder containing the source code for dwgsim, and get a fatal error: samtools/bam.h: No such file or directory

    I have tried extracting the samtools binary to the root of my home directory as suggested and creating a samtools link as suggested, but the dwgsim install script cant find it.

    Any suggestions would be helpful.

    Thanks

  • #2
    not to worry, have sorted it out

    Comment


    • #3
      Originally posted by swNGS View Post
      not to worry, have sorted it out
      Please post your answer so that others can benefit in the future.

      Comment


      • #4
        Originally posted by nilshomer View Post
        Please post your answer so that others can benefit in the future.
        Thanks! Actually I am dealing with exactly the same problem and looking forward to knowing how you made it.

        Comment


        • #5
          Most likely you need to create a symbolic link to the samtools source code, but you could post your error message or more info.

          Comment


          • #6
            Originally posted by nilshomer View Post
            Most likely you need to create a symbolic link to the samtools source code, but you could post your error message or more info.
            Thanks! It works now. What I did is put samtools folder in the dwgsim folder and then dwgsim was able to find what it needs. Though I still do not know what is wrong with the soft link.

            The error message was:
            Firstly I made the symbolic link in my home folder as an understanding of "the root directory"
            ~$ ln -s samtools-0.1.17 samtools
            ~$ cd dwgsim/
            ~/dwgsim$ make
            cd: 8: can't cd to samtools
            make[1]: Entering directory `/home/heather/dwgsim'
            cd: 8: can't cd to samtools
            make[2]: Entering directory `/home/heather/dwgsim'
            make[2]: Nothing to be done for `lib'.
            make[2]: Leaving directory `/home/heather/dwgsim'
            make[2]: Entering directory `/home/heather/dwgsim'
            make[2]: Nothing to be done for `lib'.
            make[2]: Leaving directory `/home/heather/dwgsim'
            gcc -g -Wall -O2 -o dwgsim src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o -lm -lz
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. src/dwgsim_eval.c -o src/dwgsim_eval.o
            src/dwgsim_eval.c:10:26: fatal error: samtools/bam.h: No such file or directory
            compilation terminated.
            make[1]: *** [src/dwgsim_eval.o] Error 1
            make[1]: Leaving directory `/home/heather/dwgsim'
            make: *** [all-recur] Error 1

            ################################################
            Then I made a link in the dwgsim folder
            ~$ ln -s samtools-0.1.17 dwgsim/samtools
            ~$ cd dwgsim/
            ~/dwgsim$ make
            same error messages as above.
            ~/dwgsim$ cd samtools
            bash: cd: samtools: No such file or directory
            which means I cannot cd to that link so I decided to move the samtools-0.1.17 folder in and rename it to samtools, then it worked.
            ################################################
            ~$ mv samtools-0.1.17 dwgsim/samtools
            ~$ cd dwgsim
            ~/dwgsim$ make
            make[1]: Entering directory `/home/heather/dwgsim/samtools'
            make[2]: Entering directory `/home/heather/dwgsim/samtools'
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bgzf.c -o bgzf.o
            bgzf.c: In function ‘bgzf_check_EOF’:
            bgzf.c:681:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. kstring.c -o kstring.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_aux.c -o bam_aux.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam.c -o bam.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_import.c -o bam_import.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. sam.c -o sam.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_index.c -o bam_index.o
            bam_index.c: In function ‘bam_index_load_core’:
            bam_index.c:330:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            bam_index.c:337:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            bam_index.c:350:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            bam_index.c:353:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            bam_index.c:357:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            bam_index.c:361:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            bam_index.c:371:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            bam_index.c:375:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_pileup.c -o bam_pileup.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_lpileup.c -o bam_lpileup.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_md.c -o bam_md.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. razf.c -o razf.o
            razf.c: In function ‘razf_close’:
            razf.c:815:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c:816:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c:819:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c:821:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c: In function ‘razf_end_flush’:
            razf.c:260:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c: In function ‘_razf_write’:
            razf.c:203:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c: In function ‘save_zindex’:
            razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c: In function ‘razf_open_r’:
            razf.c:422:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
            razf.c:430:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
            razf.c: In function ‘load_zindex’:
            razf.c:124:6: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
            razf.c:133:6: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
            razf.c:139:6: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
            razf.c: In function ‘razf_flush’:
            razf.c:223:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            razf.c:236:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. faidx.c -o faidx.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bedidx.c -o bedidx.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. knetfile.c -o knetfile.o
            knetfile.c: In function ‘khttp_connect_file’:
            knetfile.c:415:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            knetfile.c: In function ‘kftp_send_cmd’:
            knetfile.c:236:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_sort.c -o bam_sort.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. sam_header.c -o sam_header.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_reheader.c -o bam_reheader.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. kprobaln.c -o kprobaln.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_cat.c -o bam_cat.o
            ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
            make[2]: Leaving directory `/home/heather/dwgsim/samtools'
            make[2]: Entering directory `/home/heather/dwgsim/samtools/bcftools'
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. bcf.c -o bcf.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. vcf.c -o vcf.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. bcfutils.c -o bcfutils.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. prob1.c -o prob1.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. em.c -o em.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. kfunc.c -o kfunc.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. kmin.c -o kmin.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. index.c -o index.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. fet.c -o fet.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. mut.c -o mut.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. bcf2qcall.c -o bcf2qcall.o
            ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
            make[2]: Leaving directory `/home/heather/dwgsim/samtools/bcftools'
            make[2]: Entering directory `/home/heather/dwgsim/samtools/misc'
            make[2]: Nothing to be done for `lib'.
            make[2]: Leaving directory `/home/heather/dwgsim/samtools/misc'
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_tview.c -o bam_tview.o
            bam_tview.c:434:2: warning: #warning "No curses library is available; tview is disabled."
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_plcmd.c -o bam_plcmd.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. sam_view.c -o sam_view.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_rmdup.c -o bam_rmdup.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_rmdupse.c -o bam_rmdupse.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_mate.c -o bam_mate.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_stat.c -o bam_stat.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_color.c -o bam_color.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bamtk.c -o bamtk.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. kaln.c -o kaln.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam2bcf.c -o bam2bcf.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam2bcf_indel.c -o bam2bcf_indel.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. errmod.c -o errmod.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. sample.c -o sample.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. cut_target.c -o cut_target.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. phase.c -o phase.o
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam2depth.c -o bam2depth.o
            gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
            make[1]: Leaving directory `/home/heather/dwgsim/samtools'
            make[1]: Entering directory `/home/heather/dwgsim'
            make[2]: Entering directory `/home/heather/dwgsim/samtools'
            make[2]: Nothing to be done for `lib'.
            make[2]: Leaving directory `/home/heather/dwgsim/samtools'
            make[2]: Entering directory `/home/heather/dwgsim'
            make[2]: Nothing to be done for `lib'.
            make[2]: Leaving directory `/home/heather/dwgsim'
            gcc -g -Wall -O2 -o dwgsim src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o -lm -lz
            gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. src/dwgsim_eval.c -o src/dwgsim_eval.o
            gcc -g -Wall -O2 -o dwgsim_eval src/dwgsim_eval.o samtools/knetfile.o samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/bedidx.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/bam_cat.o -Lsamtools -lm -lz
            make[1]: Leaving directory `/home/heather/dwgsim'

            Comment


            • #7
              Having fixed the samtools binaries problem on a mac (osx), and after make went w/o a hitch, getting 'Segmentation fault' when running even the most basic command line arguments.
              Adam H. Freedman
              Dept. of OEB, Harvard University

              Comment


              • #8
                Try "make clean" then "make", but also read the README. If you still get a seg fault, please post a test case to [email protected]. The maintainer (me) is responsive.

                Comment


                • #9
                  How I fixed it... Basically it was that the sym-link to the binaries folder had to be in the root of the dwgsim folder to allow it to compile. Once that was done, the samtools binaries can be deleted.

                  Comment


                  • #10
                    Originally posted by swNGS View Post
                    How I fixed it... Basically it was that the sym-link to the binaries folder had to be in the root of the dwgsim folder to allow it to compile. Once that was done, the samtools binaries can be deleted.
                    I also have a similar problems with yours.
                    I renamed samtools-1.2 as samtools, and placed it in the root of the dwgsim folder. Then I type make. But I got this error.

                    make[1]: Entering directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
                    gcc -g -Wall -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION="0.1.11" -I. -c -o bam_index.o bam_index.c
                    bam_index.c:27:24: error: htslib/hts.h: No such file or directory
                    bam_index.c:28:24: error: htslib/sam.h: No such file or directory
                    bam_index.c:29:26: error: htslib/khash.h: No such file or directory
                    bam_index.c: In function ‘bam_index’:
                    bam_index.c:75: warning: implicit declaration of function ‘bam_index_build’
                    bam_index.c: In function ‘bam_idxstats’:
                    bam_index.c:81: error: ‘hts_idx_t’ undeclared (first use in this function)
                    bam_index.c:81: error: (Each undeclared identifier is reported only once
                    bam_index.c:81: error: for each function it appears in.)
                    bam_index.c:81: error: ‘idx’ undeclared (first use in this function)
                    bam_index.c:82: error: ‘bam_hdr_t’ undeclared (first use in this function)
                    bam_index.c:82: error: ‘header’ undeclared (first use in this function)
                    bam_index.c:83: error: ‘samFile’ undeclared (first use in this function)
                    bam_index.c:83: error: ‘fp’ undeclared (first use in this function)
                    bam_index.c:89: warning: implicit declaration of function ‘sam_open’
                    bam_index.c:91: warning: implicit declaration of function ‘sam_hdr_read’
                    bam_index.c:92: warning: implicit declaration of function ‘sam_index_load’
                    bam_index.c:101: warning: implicit declaration of function ‘hts_idx_get_stat’
                    bam_index.c:105: warning: implicit declaration of function ‘hts_idx_get_n_no_coor’
                    bam_index.c:106: warning: implicit declaration of function ‘bam_hdr_destroy’
                    bam_index.c:107: warning: implicit declaration of function ‘hts_idx_destroy’
                    bam_index.c:108: warning: implicit declaration of function ‘sam_close’
                    make[1]: *** [bam_index.o] Error 1
                    make[1]: Leaving directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
                    make: *** [all-recur] Error 1
                    [root@localhost dwgsim]# make clean
                    make[1]: Entering directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
                    make[1]: *** No rule to make target `cleanlocal'. Stop.
                    make[1]: Leaving directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
                    make: *** [cleanlocal-recur] Error 1
                    [root@localhost dwgsim]# make
                    make[1]: Entering directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
                    gcc -g -Wall -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION="0.1.11" -I. -c -o bam_index.o bam_index.c
                    bam_index.c:27:24: error: htslib/hts.h: No such file or directory
                    bam_index.c:28:24: error: htslib/sam.h: No such file or directory
                    bam_index.c:29:26: error: htslib/khash.h: No such file or directory
                    bam_index.c: In function ‘bam_index’:
                    bam_index.c:75: warning: implicit declaration of function ‘bam_index_build’
                    bam_index.c: In function ‘bam_idxstats’:
                    bam_index.c:81: error: ‘hts_idx_t’ undeclared (first use in this function)
                    bam_index.c:81: error: (Each undeclared identifier is reported only once
                    bam_index.c:81: error: for each function it appears in.)
                    bam_index.c:81: error: ‘idx’ undeclared (first use in this function)
                    bam_index.c:82: error: ‘bam_hdr_t’ undeclared (first use in this function)
                    bam_index.c:82: error: ‘header’ undeclared (first use in this function)
                    bam_index.c:83: error: ‘samFile’ undeclared (first use in this function)
                    bam_index.c:83: error: ‘fp’ undeclared (first use in this function)
                    bam_index.c:89: warning: implicit declaration of function ‘sam_open’
                    bam_index.c:91: warning: implicit declaration of function ‘sam_hdr_read’
                    bam_index.c:92: warning: implicit declaration of function ‘sam_index_load’
                    bam_index.c:101: warning: implicit declaration of function ‘hts_idx_get_stat’
                    bam_index.c:105: warning: implicit declaration of function ‘hts_idx_get_n_no_coor’
                    bam_index.c:106: warning: implicit declaration of function ‘bam_hdr_destroy’
                    bam_index.c:107: warning: implicit declaration of function ‘hts_idx_destroy’
                    bam_index.c:108: warning: implicit declaration of function ‘sam_close’
                    make[1]: *** [bam_index.o] Error 1
                    make[1]: Leaving directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
                    make: *** [all-recur] Error 1

                    ###############################################
                    Then I checked the samtools folder. There is a folder named htslib-1.2.1. Within this folder, there a folder named htslib. The problem is that I found the files hts.h, sam.h, and khash.h. I don't understand why it reported that there are no these files.

                    Thank you very much for your suggestion.

                    Comment

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