Hi Siva, You are trying to open the index file with samtools rather than the bam file. Try this instead: $ samtools view less_stringent_Ha412-34CDSHa.sorted.bam
Same goes for IGV. Point it at the .bam rather than the .bam.bai file. Regards, Chris From: Siva Nandy Date: Tuesday, 19 May 2015 11:10 To: samtools Subject: [Samtools-help] [E::hts_hopen] samtools index problem >Hi everyone, > >I've found a lot's of discussion about this problem, but haven't found the >solution. >I got this error: > >[E::hts_hopen] fail to open file 'less_stringent_Ha412-34CDSHa.sorted.bam.bai' > >[E::hts_open] fail to open file 'less_stringent_Ha412-34CDSHa.sorted.bam.bai' >samtools: failed to open "less_stringent_Ha412-34CDSHa.sorted.bam.bai" for >reading: Success > > >When I read the sorted.bam file like that: >-bash-4.1$ samtools view less_stringent_Ha412-34CDSHa.sorted.bam.bai > > >Actually I've done a bwa mapping, and trying to see my mapping results in IGV, >so need to have sorted and indexed files of bam. > >So got these: > > >-rw-rw-r-- 1 nandy inra 124K May 19 10:33 less_stringent_Ha412-34CDSHa.sam >-rw-rw-r-- 1 nandy inra 174K May 19 11:21 less_stringent_Ha412-34CDSHa.bam >-rw-rw-r-- 1 nandy inra 18K May 19 11:22 >less_stringent_Ha412-34CDSHa.sorted.bam >-rw-rw-r-- 1 nandy inra 559K May 19 11:59 >less_stringent_Ha412-34CDSHa.sorted.bam.bai > > >But when in IGV I gave the necessary there is no visualisation, so i think >it's maybe because of this error. > >regards, >Siva The University of Dundee is a registered Scottish Charity, No: SC015096 ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
