annotateRangesWithTxDb function error about fraser HOT 1 OPEN

Hi @c-mertes ,
I am having the same issue:

Error in mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",  : 
  sequence chrM has incompatible seqlengths:
  - in 'x': 16569
  - in 'y': 16571

My genome index was built using GRCh37.primary_assembly.genome.fa and gencode.v40lift37.annotation.gtf using the following:

STAR --runThreadN 10 --runMode genomeGenerate --genomeDir genome --genomeFastaFiles /data/genome/GRCh37.primary_assembly.genome.fa --sjdbGTFfile /data/genome/gencode.v40lift37.annotation.gtf --sjdbOverhang 100

My FASTQ (paired-end) were aligned to this index to obtain the BAMs used in FRASER using the following code:

STAR --genomeDir /data/blood/genome/genome --readFilesIn "$i"_1.fastq.gz "$i"_2.fastq.gz --runThreadN 16 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --chimSegmentMin 20 --quantMode GeneCounts --outReadsUnmapped Fastx --outFileNamePrefix ./star_out/"$i" --twopassMode Basic --outMultimapperOrder Random --sjdbGTFfile /data/blood/genome/gencode.v40lift37.annotation.gtf

Then, I followed the FRASER vignette but got to the same error as @ChoiJi-Hye . I am using Bioconductor version: Release (3.15).
I appreciate any feedback. Thank you.

from fraser.