Hi, community,

I am trying to run a bash file with the following, and everything works fine except I keep getting segmentation faults, Can anyone help me solve this?

Below is the bash script:

 #!/bin/bash

SECONDS=0

# Change working directory

cd "/mnt/e/Genomic learning/pipeline/RNA_Seq_pipeline" 

# STEP 1: Run FastQC

 fastqc Data/demo.fastq -o Data/

# Run Trimmomatic to trim reads with poor quality

 java -jar /mnt/f/Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 4 
 /mnt/e/Genomic/learning/pipeline/RNA_Seq_pipeline/data/demo.fastq 
 /mnt/e/Genomic/learning/pipeline/RNA_Seq_pipeline/data/demo_trimmed.fastq TRAILING:10 -phred33
echo "Trimmomatic finished running!"

fastqc Data/demo_trimmed.fastq -o Data/

# STEP 2: Run HISAT2

# mkdir HISAT2
# Get the genome indices

wget https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz

# Run alignment

 echo "HISAT2 started running!"
 hisat2 -q --rna-strandness R -x HISAT2/grch38/genome -U Data/demo_trimmed.fastq | samtools sort -o HISAT2/demo_trimmed.bam
 echo "HISAT2 finished running!"

# STEP 3: Run featureCounts - Quantification

# Get GTF

wget http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz

 echo "featureCounts started running!"
 featureCounts -s 2 -a ../hg38/Homo_sapiens.GRCh38.106.gtf -o quants/demo_featurecounts.txt 
 HISAT2/demo_trimmed.bam
 echo "featureCounts finished running!"

 duration=$SECONDS
 echo "$((duration / 60)) minutes and $((duration % 60)) seconds elapsed."

Keeping in mind I have correct directories and I evaluated the HISAT bam file with samtools and no errors appeared.

The error: "Segmentation fault" after running the feature counts, and everything else runs smoothly

thanks

It is very difficult to follow al the lines as your script content are not properly formatted.

It appears that in one command you are downloading the .GTF file into a current directory (wget http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz) and in the next command you are reading the unpacked GTF file located one directory up (featureCounts -s 2 -a ../hg38/Homo_sapiens.GRCh38.106.gtf ...). You may need to unpack the file after the wget command (gunzip Homo_sapiens.GRCh38.106.gtf.gz) and read from the current directory:

featureCounts -s 2 -a hg38/Homo_sapiens.GRCh38.106.gtf ...