Segmentation fault in samtools

[Kaskere]

I am trying to generate BAM files, however there is some error with reference indexing.

[samfaipath] build FASTA index...
[E::fai_build_core] Format error, unexpected "N" at line 1
[samfaipath] fail to build FASTA index.
./samtools_miseq.sh: line 19: 117505 Segmentation fault ./samtools view -bT $reference $file > $bamfile


here is my code

samtools faidx refseq.fasta
reference=refseq.fasta.fai
cd $INPATH

for file in $INPATH/*.sam ;
do
bname=$(basename $file ".sam")
echo $bname
bamfile=$INPATH1/$bname".bam"
namesort=$INPATH1/$bname"_namesort.bam"
fixmate=$INPATH1/$bname"_fixmate.bam"
positionsort=$INPATH1/$bname"_positionsort.bam"
markdup=$INPATH1/$bname"_markdup.bam"
cd /dir/samtools-1.10
./samtools view -bT $reference $file > $bamfile

./samtools sort -o $bamfile $file

# Add ms and MC tags for markdup to use later
./samtools fixmate -m $namesort $fixmate

# Markdup needs position order
./samtools sort -o $positionsort $fixmate

# Finally mark duplicates
./samtools markdup $positionsort $markdup
done

[HESmith]

The first error message indicates that your reference genome is the culprit. Some versions contain 'N's that correspond to placeholders for the telomeric repeats. This causes reference indexing to fail, which in turn results in the segmentation fault.