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
