SAMTOOLS SORT error

Question

[bioinfo]

I am currently using the samtools sort feature, and have created nine sorted bam file. By the time the last ninth file was created, strange hieroglyphs came out and can not be stopped at the terminal. Can I just close the terminal window and proceed to the next step? Thank you for answering

Answer 1

[John Marshall]

The strange hieroglyphics are your sorted output, and the nine files you saw are temporary files used during sorting. Time to reread the manual:

The sorted output is written to standard output by default, or to the specified file (out.bam) when -o is used. This command will also create temporary files tmpprefix.%d.bam as needed when the entire alignment data cannot fit into memory (as controlled via the -m option).

Answer 2

[WouterDeCoster]

Please add the command you used and the version of samtools you have installed. But it's highly likely that something went wrong and you should repeat the sorting. Make sure you have enough disk space available.

[bioinfo]

I have two contigs to be analyzed. So my workflow like this : I've two fasta file(chromosome1, chromosome2) and do bowtie2-build each genome. and aligned reads to each genomes, respectively Maybe, I think there's no reads aligned due to separate process. So do I merge the Fasta file in one?

[WouterDeCoster]

And what's the connection between your original question and this?

[Pierre Lindenbaum]

What Wouter said:

Please add the command you used and the version of samtools you have installed

[bioinfo]

my samtools version is 0.1.19

[GenoMax]

That version is ancient. You should upgrade to the latest.

[bioinfo]

Oh, It works. Thank you so much.