samtools crashes when sorting files

Question

[yomogy]

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.

[Pierre Lindenbaum]

for i in *.sam

you should learn about make and about workflow managers (nextflow, snakemake....)

[Pierre Lindenbaum]

, gibberish letters show up and crash in the middle.

is there any space in the filenames ? protect the filenames with quotes:

set -x
for i in *.sam
do
echo "RUNNING $i" 1>&2
samtools sort -T "$i.tmp"  -O BAM -o "$i.sorted.bam" "$i"
samtools index "$i.sorted.bam"
done

[yomogy]

Thank you for your reply.

I got error message saying

• can't parse output format "BAM"
• "fail to open file output.bam" <- I got this message whenever I ran "samtools sort -o output.bam input.sam" (I don't know I need to put "input.sam" right after "sort")

[Ram]

What version of samtools are you using?

[GenoMax]

1.2 according to original post. So older.

yomogy : Latest version is 1.16. It may feel odd but 1.2 is not the latest. It goes 1.1, 1.2,1.3 and so on.

[Istvan Albert]

add an echo in front of each samtools command, then send us the resulting output

PS. if you have only four samples, just run them manually :-) or add the commands to a text file manually

then run

bash myfile.txt

see if they crashes that way as well

Answer 1

[Pierre Lindenbaum]

can't parse output format "BAM"

remove -O BAM . Your samtools is too old.

[yomogy]

Thank you very much, it works!