Few Successfully assigned alignments

[swmuyu]

Issue Description:
When i use the Count_matrix.sh to transform the row data, I run this step "featureCounts -t exon -g gene_id -a $gtf -o gene_assigned_gene -R BAM $sample.Aligned.sortedByCoord.out.bam -T N". There are very few Successfully assigned alignments. Is it because i use the gtf file incorrectly. Are the $gtf and $sjdbGTFfile same file ?

|| Process BAM file SRR13970434.Aligned.sortedByCoord.out.bam... ||
|| Single-end reads are included. ||
|| Total alignments : 31140514 ||
|| Successfully assigned alignments : 250860 (0.8%) ||

[SMU-TK-2022]

How did you successfully run anchoradp.o without the "Segmentation fault" error?
Thank you for your help.