Question: bam_sort_core problem when bam files be processed by samtools
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1106518271 • 60 wrote:
I sorted my RNA-Seq bam files after mapping by star, and here is my key command line in a for cycle bash file:
samtools sort $file -o ${filename}.sorted.bam
At last, the one error file shows like:
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
[bam_sort_core] merging from 7 files and 1 in-memory blocks...
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
[bam_sort_core] merging from 5 files and 1 in-memory blocks...
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
[bam_sort_core] merging from 13 files and 1 in-memory blocks...
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
[bam_sort_core] merging from 2 files and 1 in-memory blocks...
...
Something wrong here? I searched but still don't know why, so I'm not sure these sorted files be used for next step?
What's more, I have M(like 63) files, and there M-N(like 6, yes, few) lines, it means not all file will meet this problem? It makes me more confused.
Any ideas will be appreciated!!!
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modified 7 months ago
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linouhao • 0
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8 months ago by
1106518271 • 60
If you have the memory, you can reduce the number of temporary files by increasing the default memory usage from 768Mb to, say, 2G using the
-moption, e.g. samtoolssort -m 2G -o out.bam in.bam. Be sure to never use something like-m 2rather than-m 2Gas this would set the memory limit to 2 bytes resulting in thousands of tmp files, eventually crashing the system.Got it, many thanks!
so is it really an error, and anyone knows to set -@ and -m, which is more useful when dealing with hundreds of bams at the same time in cluster, thanks a lot
Please use
Add Commentfor comments. As Istvan explained, these are just status messages, neither errors nor warnings. Set -@ and -m as you like, but these are options that still deal with one file at a time. If you want things parallelized, have a look at GNU parallel, like:This command will sort all BAM files in your current directories, 8 at a time with 2 cores and 2GB of memory per core each.
By the way, will this "error" here lead to give wrong result(${filename}.sorted.bam)?