Samtools sort crash

Question

[saaz1291]

Hi, I am trying to use samtools to sort my bam files: samtools sort <name>.bam -o <name>_sorted.bam.

After a while, the terminal seems to crash. I have linked screenshots of both the terminal window and the system monitor. The problem seems to start around the 15s mark in the system monitor.

http://imgur.com/a/ADoTY

https://imgur.com/J31YJ3o

I have tried this with a variety of bam file sizes, from 10 MB to 500 MB (made from sam files of 35 MB and 3 GB respectively). I have also tried using less memory (-@ 1 -m 3G). But the problem occurs in each one. I can see some temp files but not the final output.

[lshepard]

Hi, I can't see the screenshots. Make sure you added them or output the error here.

Edit: Ok thanks for adding. The screenshots are not too helpful. It is much easier if you add a reproducible example of your issue, along with the error message that should come up.

By the way, I am guessing that by your screenshot you are trying to view the bam file. This will not be possible if you just open as it is a binary file. You can see it with samtools with the following: samtools view -h file.bam | less

[saaz1291]

Hi, I edited the post to include the links. Thanks for pointing that out!

[saaz1291]

So, the problem is that the whole gibberish on the screen ends, by itself with no particular error message, and I can actually type in more commands on the terminal. But the temp files remain in the directory, and the expected output file never appears.

http://imgur.com/a/lnRX2

That is what it looks at the end.

Edit: This happens not when I'm viewing the file, but just running the sort command.

[lshepard]

You may want to run the process in the background through a screen session for example. Could be that this is just timing for some reason.

Answer 1

[Pierre Lindenbaum]

my guess: You're using an old version of samtools but you're using the arguments of the new version. (or vice/versa)

http://www.htslib.org/doc/samtools-0.1.19.html

vs

http://www.htslib.org/doc/samtools.html

[saaz1291]

Thanks! That was it!