Hi,

I am processing ChIP sequencing data. I mapped FASTQ files using Bowtie2 then I tried to convert sam files to bam files, then sort and index the files using samtools. When I try to sort the bam files, gibberish letters show up and crash in the middle. I have total four files but I got the same error in all four files (all files were downloaded from publicly available data). I used samtools 1.2 this time(server in my university installed samtools1.2), I also used samtools 1.12 on the laptop computer, the same error occurred.

The code I used was:

for i in *.sam
do
  samtools view -b -S $i -o $i.bam
  samtools sort $i.bam -o $i.sorted.bam
  samtools index $i.sorted.bam
done

I also tried:

for i in *.sam
do
  samtools sort $i -o $i.sorted.bam
  samtools index $i.sorted.bam
done

but the same result.

These codes worked in the past, and I could not figure out where the problem is.