Entering edit mode
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