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Using samtools sort to convert .sam files to .bam files

Hi all, I am using the following command to convert .sam files to .bam files:

samtools sort -@ 8 -o SampleID.bam SmapleID.sam

The standard error files usually start with something like "merging from 16 (this number varies) files ..." I was wondering what the number means.

Also, for several of my samples, I got messages saying that "merging from 0 files..." Does it indicate that the resulting .bam files do not contain any alignment information?

Any input?

Thank you very much.

rna-seq alignment
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by H.LU11 • H.LU11

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

• 1 views • link
written by Ram Ram

Thank you for formatting the code for me.

• 1 views • link
written by H.LU11 • H.LU11

Note that if what you are really after is sam - bam conversion, its must faster to use samtools view (but it doesn't sort obviously).

• 1 views • link
written by Carlo Yague Carlo Yague

1 answer

merging from 16 (this number varies) files

when the number of reads cannot fit in memory, the tool need to sort on disk. https://en.wikipedia.org/wiki/External_sorting

those '16 files' are the temporay chunks of data stored on disk.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre, thank you for the information. If the size of the .sam files are small and can fit in the memory, is it possible to have zero temporary chunks of data? Thank you.

• 1 views • link
written by H.LU11 • H.LU11

see option -m

 -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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