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6.3 years ago
bioinfo
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I'm using "samtools sort" to arranging bam to sorted bam my command line was : samtools sort sample.bam -o sample.sorted.bam -m 3000000000
But result command line is : [bam_sort_core]merging 1 files and 1 in-memory blocks...
Is it normal statement when using samtools sort?
I think by specifying the max memory per thread so high, you told it to hold the whole file in memory at once.
This doesn't look like an error to me, just a progress message.
In addition, I changed your title to small letters. There is no need to SHOUT ;-)
Have you tried to sort without specifying memory option? That may not be needed.
The memory option is not required. The default is much lower, which is why that message usually indicates that multiple files are being merged.