Question: Segmentation fault Freebayes
0
gravatar for luzglongoria
7 months ago by
luzglongoria40
luzglongoria40 wrote:

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 :)

ADD COMMENTlink written 7 months ago by luzglongoria40

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

ADD REPLYlink written 7 months ago by ATpoint36k

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?

ADD REPLYlink written 7 months ago by luzglongoria40

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.

ADD REPLYlink modified 7 months ago • written 7 months ago by ATpoint36k

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
ADD REPLYlink modified 7 months ago • written 7 months ago by luzglongoria40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1990 users visited in the last hour