Samtools sort output many files

[LacquerHead]

Hi trying to figure out what I am doing wrong sorting some BAM files with the following command and the output instead of a single sorted BAM file is many individual files, any help is appreciated!

samtools sort -@ 12 -m 2 297422_S2_R1.bam 297422_S2_R1.sorted.bam

[GenoMax]

Samtools sort makes several temporary files while the sort operation is in progress. If those temp files did not get cleaned up then it is likely that the sorting did not complete properly. One cause may be the storage filled-up (or you hit disk quota etc). There is an option to specify a different location for those temp files (if the current directory does not have enough space).

[jmarshall]

You're telling samtools it may only use quite a small memory buffer, so it is using many many temporary files instead. You may wish to reread the documentation and use (say) `-m 2G` instead.

(We've added an error message that will be in the next version of samtools that refuses to continue if a ridiculously small buffer is specified.)

[LacquerHead]

Sorry forgot to mention I am running this on a cluster using the following, so splitting:

#!/bin/bash
#$ -S /bin/bash
#$ -v LD_LIBRARY_PATH
#$ -cwd
#$ -l m_mem_free=2G
#$ -pe threads 12

You're telling samtools it may only use quite a small memory buffer, so it is using many many temporary files instead. You may wish to reread the documentation and use (say) `-m 2G` instead.

(We've added an error message that will be in the next version of samtools that refuses to continue if a ridiculously small buffer is specified.)