SetMateInformation: Input is not queryname sorted or grouped

[sofiapuvogelvittini]

Hi, Thanks for your great package. I have paired end RNA seq data, with three fastq files per samples. I used Hisat2 to align R1 and R2 reads, and then I used AnnotateBamWithUmis to include the UMI (R3) in the RX flag of the bam file. Next, I used samtools sort to sort the bam files. Now, I want to use GroupReadsByUmi, however, it indicates that I miss the mate mapping quality tag. Thus, I was trying SetMateInformation to include the MQ, but I obtained the following error "Input is not queryname sorted or grouped ". My bam files are already sorted with samtools sort, so I am not sure what this error mean and also I don't know how to fix it. Would you please help me with this? Best regards and thanks a lot, Sofía