Samtools sort results are different
samtools view -bhq 20 -@ 16 ./${sample}.sam | \
samtools sort -m 5G -@ 16 -o ./${sample}.bam
The following results were obtained
starting new job with ongoing=0
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
However, when the same method is used for different samples, only the following results appear
starting new job with ongoing=0
I don't know why, how can I find the problem?
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Hang on, are the results different or is the log different?
It's all different. Without
[bam_sort_core]that line of information,we would have got BAM files of more than 100kb, but we got BAM files of 20KB and 30Kb.Another strange point is that for the same sample, when I use the reference genome of the whole genome, there will be two lines of information
In the mitochondrial reference genome, there is only one line of information
and there is no other information.
Try
echo-ing$samplebefore each command. I have a feeling$sample.samis doing something unexpected.