Hi James, Are the output files growing in size, or stuck? That might help identify a problem.
But also, are you really using samtools 1.3.1 (released December 2015), which is over three years old? If so, it could easily mean a problem with the older version - I would try updating to 1.9 which was released summer 2018. Peter On Thu, Jan 24, 2019 at 7:35 AM James Jacobs <jaco...@ohsu.edu> wrote: > > Hello, > > I am attempting to convert a BAM file to a CRAM file in order to cut down on > storage needs. The program has been running for over 3 days now and I'm > wondering if that is to be expected or if I did something wrong. > > I am running samtools-1.3.1 and I used the following command > > samtools view -T <path to reference .fasta> -C -o <path to output .cram file> > <path to input .bam file> > > The input .bam file is about 96Gb. > > Thanks for your help. > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
