I run follow Command-line code:

Linux (Ununtu 22.04.5 LTS in Whidows WSL)

hisat2 -p 6 --dta -x /mnt/d/hiv_omics/scripts/Hisat2_index/genome_tran  -U /mnt/d/hiv_omics/GSE180044/SRR15127754/trimmed_output/SRR15127754_trimmed.fq.gz  -S /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_align.sam

samtools view -@ 8 -bS /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_align.sam | samtools sort -@ 8 -o /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_align.sorted.bam

samtools markdup -@ 8 -r -s /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_align.sorted.bam /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_align.dedup.bam

featureCounts -T 8 -t exon -g gene_id -a /mnt/d/hiv_omics/scripts/Homo_sapiens.GRCh38.114.gtf --primary -o /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_counts.txt /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_align.dedup.bam

In the final step (featureCount), the report error is: buffer overflow detected : terminated Aborted (core dumped)

How can I solve it. Thanks. Rui Tang

Hi Rui Tang,

The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to truncation or parsing issues when accessed via WSL's /mnt/d mount. First, verify the GTF integrity:

zcat /mnt/d/hiv_omics/scripts/Homo_sapiens.GRCh38.114.gtf.gz | tail -n 20

Ensure the final lines are complete (no mid-line cutoff). If suspect, redownload the GTF and keep it within the WSL filesystem (e.g., ~/annotations/). Then rerun:

featureCounts -T 8 -t exon -g gene_id -a ~/annotations/Homo_sapiens.GRCh38.114.gtf --primary -o /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_counts.txt /mnt/d/hiv_omics/GSE180044/SRR15127754/alignment/SRR15127754_align.dedup.bam

If the error persists, reduce threads to 4 or run on a native Linux partition.

Kevin