I must first compliment you on your question, you show the commands you tried and the resulting error messages :^)
I tried with one of my bam files, and the problem was the "-b" parameter. If you omit this then it will index successfully. It seems this is a difference with samtools versions, version 0.1.19 behaves as you show, the version 1.2 will work with the -b parameter On 12/04/2015 12:13 PM, Yampolsky, Lev wrote: > Dear Colleagues - > > > Any ideas? Is the file maybe too large? > > The file Epi38All.bam was created by samtools merge -r Epi38All.bam ./*.bam > > > ly@etsu906119:/Volumes/MyBook/Epi13_38/BAM$ samtools index -b Epi38All.bam > > open: No such file or directory > > [bam_index_build2] fail to open the BAM file. > > ly@etsu906119:/Volumes/MyBook/Epi13_38/BAM$ samtools index -b > /Volumes/MyBook/Epi13_38/BAM/Epi38All.bam > > open: No such file or directory > > [bam_index_build2] fail to open the BAM file. > > ly@etsu906119:/Volumes/MyBook/Epi13_38/BAM$ ls -l Epi38All.bam > > -rw-r--r-- 1 ly staff 200G Dec 4 00:14 Epi38All.bam > > > Thank you very much in advance! > > -- > Lev Yampolsky > > > Department of Biological Sciences > East Tennessee State University > Box 70703 > Johnson City TN 37614-1710 > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > > ------------------------------------------------------------------------------ Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
