After running samtools, the featureCounts command crashed.
0
0
Entering edit mode
Rui • 0
@04ff3e59
Last seen 23 days ago
Hong Kong

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

RNASeqData Bioconductor RNASeq • 90 views
ADD COMMENT

Login before adding your answer.

Traffic: 1155 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6