Cannot create the sorted sam using samtools sort

Question

[wyxhiter]

Hello guys. I met some problems when I tried to follow the tutorial of Nanopolish in https://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html

One of the steps is to use samtools to sort alignments. Here I got a reads.bam file, and try to sort it into reads.sorted.bam file. My environment is Utubun and the version of samtools is 1.9 (the most recent one).

I run the following command

samtools sort -o reads.sorted.bam reads.bam

Error: samtools sort: couldn't allocate memory for bam_mem

Folowing the suggetion from https://github.com/samtools/samtools/issues/831 Then I try to run

 samtools sort -m GALAXY_MEMORY_MB / GALAXY_SLOTS -o reads.sorted.bam reads.bam

Output information:

Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
             Number of additional threads to use [0]

For me, now it seems no error occur... However, I could not find the reads.sorted.bam in the current directory... so when I run the next step,

samtools index reads.sorted.bam

Expected error occurs: samtools index: failed to open "reads.sorted.bam"; No such file or directory.

I really dont understand what happened. Can anyone help me to find out why I could not create the sorted bam file? Thank you.

Answer 1

[Pierre Lindenbaum]

Error: samtools sort: couldn't allocate memory for bam_mem

use option -m (-m INT Set maximum memory per thread; suffix K/M/G recognized [768M])

to reduce the memory. For example : '-m 10M' but it looks like your computer hasn't enough memory...

[wyxhiter]

Thank you! I changed to 10M and can have an output file now. Yes... I have checked the free memory, only 87M are left... I use VirtualBox for operating Ubuntu...

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

[wyxhiter]

Noted with thanks, I have accepted the answer from Pierre :)