Hi, I am having a weird error with samtools rmdup on paired end data:
$ samtools rmdup file.bam file.bam.rmdup [bam_rmdup_core] 1 unmatched pairs *** Error in `samtools': free(): invalid next size (fast): 0x0000000001099af0 *** Aborted (core dumped) First I do not understand why I would have 1 unmatched pair as flagstat tell me I have none: $ samtools flagstat file.bam 28075120 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 28075120 + 0 mapped (100.00%:-nan%) 28075120 + 0 paired in sequencing 14037560 + 0 read1 14037560 + 0 read2 28075120 + 0 properly paired (100.00%:-nan%) 28075120 + 0 with itself and mate mapped 0 + 0 singletons (0.00%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) and I do not understand the error *** Error in `samtools': free(): invalid next size (fast): 0x0000000001099af0 *** Anybody would have an idea? -- Samuel COLLOMBET PhD student Computationnal systems biology Lab (Pr. Thieffry) Institut of Biology at the Ecole Normale Superieure 46 rue d'Ulm - 75005 Paris FR ------------------------------------------------------------------------------ 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 Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
