I'm trying to learn about CRAM files and CRAMtools and have been running through a tutorial given to me by a colleague. No one seems to understand the problem I'm having so I hoped the kind Biostars community might be able to help! Put simply, CRAMtools is not downloading appropriate reference FASTA files as I would expect it to.
I am using a CRAM file I found here, specifically the one named '12216_4#69.cram'. I then try to acquire the reference sequence for this using the following command: cramtools getref -I 12216_4#69.cram -F shigella_sonnei.fa That is a capital 'i' so that's not the problem. The output I get looks like this:
>gi|74310614|ref|NC_007384.1| 65f3aba8874596edd150cf2a83033bd3
Note the conspicuous lack of sequence! Interestingly, that checksum value on the end does point to the genome of the species I expect it to. I tried downloading the genome myself and just using that for further sections of the tutorial, but CRAMtools didn't want to work with it. I thought there might be something up with the original CRAM file itself so I tried another CRAM file, available here, which is used as an example file in the ENA's own tutorial here. When running the getref command on it, I get a similar result:
>phix-illumina.fa bb9dae7b38a25a45dae8e3179d7c4241
I was initially using CRAMtools 3.0 but have since repeated all of the above using CRAMtools 2.0, and received the same results. If anyone knows anything about this, I'd be grateful to hear from you. Or even if you could check the files yourself and tell me if it does appropriately download the reference file, that would be useful information.
