Segmentation fault Freebayes

Question

[luzglongoria]

Hi friends,

I have been working on my reads in order to detect the SNP by using a reference genome.

What I have done is:

# construct the FM-index for the reference genome 
bwa index ref.fa

# Find the SA coordinates of the input reads
bwa aln ref.fa short_read.fq > aln_sa.sai

# Generate alignments in the SAM format given paired-end reads
bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam

# Transform .sam files into .bam files
samtools view -b -o output.bam input.sam

# Merge all the.bam files into one
samtools merge total.bam aln-pe_1.bam aln-pe_2.bam aln-pe_3.bam 

# Run Freebayes 
freebayes -f genome.fa total.bam >new.freebayes.vcf

But when I run the last command I get this simple error:

Segmentation fault (core dumped)

It generate a .vcf file but empty.

What is the problem? is it the software? or the .bam file?

If, for example, I do:

head aln-pe_1.sam

@SQ SN:NW_007931122.1   LN:88717973
@SQ SN:NW_007931123.1   LN:67421796
@SQ SN:NW_007931124.1   LN:55561340
@SQ SN:NW_007931125.1   LN:50638526
@SQ SN:NW_007931126.1   LN:74395783
@SQ SN:NW_007931127.1   LN:45578592
@SQ SN:NW_007931128.1   LN:42072568
@SQ SN:NW_007931129.1   LN:30842146
@SQ SN:NW_007931130.1   LN:36511336
@SQ SN:NW_007931131.1   LN:27271039

Any help would be more than welcome :)

[ATpoint]

Is the command running before? Check with top, and how much memory do you have?

[luzglongoria]

It is the first time I run freebayes. I am running in a local server (not in my computer) which is shared. I know some other collegues have run freebayes on it properly. May be is a problem of the size of my samples?

[ATpoint]

I meant if the command runs after starting it and then crashes after e.g. a few minutes or dies it get killed right away? Also, how much memory? Run it again and monitor using top.

[luzglongoria]

I run it and after 5 seconds it dies... About the memory

df -h

System load:    4.56    Local Users:    7
Memory usage:   0.0%    System uptime:  54 days
Usage on /home: 73% Swap usage: 0.0%

    Filesystem                             Size  Used Avail Use% Mounted on
    /dev/mapper/vg_geneiousserver-lv_root  129G   14G  109G  12% /
    devtmpfs                               252G     0  252G   0% /dev
    tmpfs                                  252G     0  252G   0% /dev/shm
    tmpfs                                  252G  115M  252G   1% /run
    tmpfs                                  252G     0  252G   0% /sys/fs/cgroup
    /dev/sdc1                              477M  287M  162M  64% /boot
    /dev/sdh1                              9.8T  6.7T  2.6T  73% /home
    /dev/mapper/vg_data-data               3.2T   86G  3.0T   3% /home2
    /dev/mapper/vg_data-home               2.0T  373G  1.6T  20% /var
    tmpfs                                   51G   12K   51G   1% /run/user/42
    tmpfs                                   51G     0   51G   0% /run/user/1028
    tmpfs                                   51G     0   51G   0% /run/user/1020
    tmpfs                                   51G     0   51G   0% /run/user/1051
    tmpfs                                   51G     0   51G   0% /run/user/1044