Fix samtools sort memory failures and OOM kills

TL;DR

For ") sorts cannot be indexed ": use this skill when you run into "Fix samtools sort memory failures and OOM kills". For ") sorts cannot be indexed ": almost every samtools sort memory failure is one of four distinct problems with different fixes. Classify from the observable evidence FIRST, then apply the fix for that class.

TL;DR

For ") sorts cannot be indexed ": almost every samtools sort memory failure is one of four distinct problems with different fixes. Classify from the observable evidence FIRST, then apply the fix for that class. From the man page: > -m INT, Approximately the maximum required memory per thread, > specified either in bytes or with a K, M, or G suffix. [768 MiB] So samtools sort -m 5G -@ 12 requests up to ~60 GiB (5 GiB × 12 threads), not 5 GiB.

) sorts **cannot be indexed** —

When to use

You are seeing this: samtools sort -m is per thread, not total. Use this skill when you run into "Fix samtools sort memory failures and OOM kills".

When not to use

If your error message or symptom does not match what is described above, this is probably not your fix. Search for your exact error text instead of forcing this one to fit.

Versions

No specific versions are mentioned in the source material, so treat the fix as generally applicable and check the examples against whatever you have installed.

Use this when samtools sort dies with couldn't allocate memory for bam_mem, when the shell reports Killed (OOM killer), or when a sort pipeline stalls or fills the disk with temp files. Almost every samtools sort memory failure is one of four distinct problems with different fixes. Classify from the observable evidence FIRST, then apply the fix for that class.

0. The one fact that explains most failures

samtools sort -m is per thread, not total. From the man page:

-m INT, Approximately the maximum required memory per thread, specified either in bytes or with a K, M, or G suffix. [768 MiB]

So samtools sort -m 5G -@ 12 requests up to ~60 GiB (5 GiB × 12 threads), not 5 GiB. This is the single most common cause of Biostars "sort ran out of memory" threads: the declared -m looked reasonable, but multiplied by -@ it exceeded the machine or the job's memory limit.

Compute the real request before touching anything:

total ≈ (-m value) × (-@ threads)

1. Classify the failure

A. samtools sort: couldn't allocate memory for bam_mem

The sort's per-thread allocation failed. Compare -m × -@ against actual available RAM (free -g):

• If -m × -@ exceeds free RAM (or the scheduler/Slurm/Nextflow memory limit for the job): over-requested memory. Fix: lower -m, lower -@, or both so the product fits. Example on a 32 GiB node:

  samtools sort -m 2G -@ 8 -T /scratch/sort_tmp -o sorted.bam in.bam
  # 2G x 8 threads = ~16 GiB, comfortably inside 32 GiB

• If -m × -@ fits easily yet allocation still fails: suspect the machine is actually smaller than you think (a VM resized to MB instead of GB is a real Biostars case) or another process holds the memory. Check free -g and dmesg | tail for the truth.

B. Shell prints Killed / exit code 137 / line N: [PID] Killed samtools sort

That's the Linux OOM killer (or the scheduler killing an over-limit job), not samtools failing cleanly. Same fix as A, the product -m × -@ is too big plus check the scheduler: in Nextflow/Slurm/SGE the job's declared memory (e.g. memory '32 GB') is the limit, not the node's RAM. Size the sort to the declared memory:

# nextflow process declaring 32 GB / 8 cpus:
samtools sort -m 3G -@ 8 -T ./sort_tmp -o out.bam in.bam
# 3G x 8 = ~24 GiB, under the 32 GB declaration with headroom

Splitting one process into two sequential sorts does not help an OOM: each sort's -m × -@ is what matters, not how many sorts ran.

C. No space left on device / sort stalls with growing temp files

When the data doesn't fit in -m × -@, sort spills to temp files named [tmpprefix].NNNN.bam in the -T directory, then merges them single-threaded at the end. Two sub-causes:

1. The -T directory is full or tiny. /tmp is often a tmpfs physical RAM, not disk, so -T /tmp on a big sort burns RAM twice (sort buffers and temp files) and then fails. Point -T at a real scratch filesystem with free space:

   mkdir -p /scratch/$USER/sort_tmp
   samtools sort -m 2G -@ 8 -T /scratch/$USER/sort_tmp -o sorted.bam in.bam

Check with df -h on the -T directory before the sort.

2. -m is far too small for the data, so sort creates thousands of temp files and the final merge crawls. Raise -m (keeping the product under available RAM) instead of lowering it. If you can't raise -m, accept the slow merge, lowering -m further makes it worse.

D. Name-sort (-n) pipelines OOM where coordinate sorts don't

samtools sort -n (name sort, used before fixmate/markdup) needs substantially more memory than a coordinate sort on the same file. If only the -n stage fails:

• Give the -n stage a bigger -m than the coordinate stage, or

• use samtools collate instead: the man page notes "Consider using samtools collate instead if you need name collated data without a full lexicographical sort", collate is designed for exactly the fixmate/markdup input pattern and uses less memory.

Also remember: -n (and -t) sorts cannot be indexed, samtools index requires coordinate sort. If a downstream tool complains about a missing index, the fix is a second coordinate sort, not re-running the name sort.

2. Rules of thumb

• Default -m is 768 MiB per thread. On a modern node, 4 8 threads at 1 2 GiB each (-m 2G -@ 4) sorts most BAMs fast; more threads help up to the disk's write bandwidth, then stop helping.

• -m has a floor of 1M (sort enforces it to avoid a temp-file explosion).

• Always set -T explicitly to a scratch dir with space; never rely on /tmp on shared systems.

• Verify the sorted result: samtools view -H sorted.bam | grep '^@HD' should show SO:coordinate (or SO:queryname for -n), and samtools quickcheck sorted.bam should exit silently.

Quick decision tree

1. couldn't allocate memory for bam_mem → compute -m × -@ vs free RAM → lower -m/-@.
2. Killed / exit 137 → same math, but against the job's declared memory (scheduler/Nextflow), not the node.
3. No space left on device or endless temp files → -T on real scratch disk (df -h first); don't use tmpfs /tmp.
4. Only -n fails → bigger -m for that stage, or samtools collate.
5. Merge phase slow but progressing → -m too small; raise it if RAM allows.

Built from the samtools sort man page (-m is approximately the maximum required memory per thread, default 768 MiB; -T temp-file behavior; -n incompatible with samtools index; samtools collate as the name-collation alternative) and recurring Biostars threads on sort memory failures in Snippy and Nextflow pipelines.