I would suggest comparing the MD5 (or SHA256) checksums of the input files. My guess is a Windows vs Linux new line ending change during a file transfer could have thrown some things off, or a rarer network glitch is possible too. It should be easy to check and rule this out.
If they match perfectly, then I would next look at the exact versions of samtools in use by the two groups. Peter On Tue, Jan 18, 2022 at 5:44 PM Sabine van Schie <sabinevsc...@gmail.com> wrote: > Hi all, > > I used samtools index to index cram files and tried to view the data in > the Integrated Genomic Viewer ( > https://software.broadinstitute.org/software/igv/). The samples are > whole-genome sequencing data from S. cerevisiae. > > We have downloaded the cram files from our collaborator and I have simply > used the default samtools index command to index the cram file. I did not > get any errors at this stage. > > For some files I'm having problems viewing certain parts of the genome. > However, for other files (from the same batch and using the same ref genome > and alignment method), I can view the exact same region just fine. The > error in IGV is as follows: > > Error - possible sequence mismatch (wrong reference for this file): > htsjdk.samtools.cram.CRAMException: Reference sequence MD5 mismatch for > slice: sequence id 10, start 1, span 666454, expected MD5 > c831338ca9079d76bebd0b0a5eb102ef > > I have attached one cram index file that gives this error when looking at > e.g. YKR002W on Chr XI. I haven't attached the corresponding cram file > because it is rather large (200 MB), but if needed I can try to send this > or other info that is missing. > > Since I'm new to the cram format, and samtools in general, I'm not sure > whether the issue arises during the indexing with samtool and how I could > check this. > > I would be very happy with any troubleshooting tips! > I'm using: samtools 1.14 Using htslib 1.14. > > > Thanks, > > Sabine > > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help >
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