Hi Guillermo, Yes, certainly if you're running out of space then that could cause the problem. In fact, given the context, that's probably likely.
BTW, if those BAM files are from tophat, then the merged BAM file should still be sorted (even if the header doesn't say so). 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 4:32 PM, Guillermo Parada <gepar...@uc.cl> wrote: > Hi Devon: > > Thanks for quick answer! > > I do not use windows to work (the world would be better if everybody > follow this rule). I'm working by ssh on a Ubuntu 11.04 machine. I > didn't know if I had installed zlib, so I just installed zlib-1.2.8. > But, I'm getting the same compile error. > > Since a long time that I'm working with samtools and this is the first > time that I have this EOF warning. I was trying to merge and sort a > lot of BAM files, do you think that this is related with the EOF > warning? I'm thinking that maby I got out of disk space Do you think > that this is a posible explanation for a EOF warning? > > I'm interest in solving either the EOF warning or the compile error to > keep working. Thanks you so much for your help! > > > 2014-11-10 12:12 GMT-03:00 Devon Ryan <dpr...@dpryan.com>: > > 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 > > > > 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 > > > > > > > > -- > Guillermo Parada > > > Biochemist, assistant research scientist > Pontificia Universidad Católica de Chile >
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