I am trying to convert a cram to a bam using the following samtools command set-up:
samtools view -h -b -@ 16 file.cram -o file.bam -T reference.fa 2>&1 | tee -a log.txt
However, when I try this, I get the following error:
[E::cram_get_ref] Failed to populate reference for id 76 [E::cram_get_ref] Failed to populate reference for id 102 [E::cram_get_ref] Failed to populate reference for id 129 . . . . [continues for over 20 lines like this]
I'm not sure why I am getting this error. I've made sure to use the same reference file that was used to generate the cram (I was using a different reference file before) and have also included the reference.dict file.
It's also noteworthy that, although I'm getting this error, the cram file still gets converted to a bam and downstream processes like GATK are still able to run on the bam. It's just concerning to be getting such an error message. Any thoughts?