Hi Guillermo, Yeah, some of the older versions always used to incorrectly give the EOF warning when you used a pipe as input. That was quite annoying.
The compilation error is due to the linker not being able to find a function that should be provided by zlib. What version of zlib do you have on your computer (and are you by chance using windows)? Regards, Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Laboratory for Molecular and Cellular Cognition German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn Germany <devon.r...@dzne.de> On Mon, Nov 10, 2014 at 4:01 PM, Guillermo Parada <gepar...@uc.cl> wrote: > Hello! > > Since a few day that I'm trying to solve this problem. I'll thanks you > so much I you help me with this. > > > Using the old version of samtools I'm constantly having this error: > > samtools merge - SRR*trim/accepted_hits.bam | samtools sort - TOTAL2 > > [bam_sort_core] merging from 839 files... > [bam_header_read] EOF marker is absent. > [bam_header_read] EOF marker is absent. > [bam_header_read] EOF marker is absent. > [bam_header_read] EOF marker is absent. > [bam_header_read] EOF marker is absent. > [bam_header_read] EOF marker is absent. > [bam_header_read] invalid BAM binary header (this is not a BAM file). > Segmentation fault > > > So now I want to update samtools hopping to solve this issue. But when > I try to compile the new version of samtools from the source I'm > getting this error: > > make > gcc -pthread -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o > bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.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 padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o > bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o > bam_tview_html.o bam_lpileup.o libbam.a htslib-1.1/libhts.a -lcurses > -lm -lz > htslib-1.1/libhts.a(zfio.o): In function `zfpeek': > /home/geparada/Downloads/samtools-1.1/htslib-1.1/cram/zfio.c:97: > undefined reference to `gzgetc_' > collect2: ld returned 1 exit status > make: *** [samtools] Error 1 > > > What should I do? > > I'm really stacked... > > > Thanks for your time! > > -- > Guillermo Parada > > > Biochemist, assistant research scientist > Pontificia Universidad Católica de Chile > > > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help >
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