[Samtools-help] samtools sort segmentation fault

[Marie K. <mkr...@cn...>]

Hello all,

I have metatranscriptome data that I have mapped to a metagenome using 
bowtie2 with no problem. I used samtools view to convert the output sam 
file to a bam file with no errors and am now trying to sort my bam 
files. Unfortunately, I keep getting a segmentation fault error and the 
core is dumped.

This is the my command line input:
samtools sort FIIA01MTMAP_try2.bam FIIA01MTMAP_sorted

This is the output:
[bam_sort_core] merging from 107 files...
Segmentation fault (core dumped)

It creates 107 temporary files, but is unable to merge them into one 
sorted file. I am using samtools version 1.2.
Also, in case this matters, my bam files are rather large ranging from 
17-34 GiB.

Please help.

Regards,
Marie