Floating point exception

[aquaskyline]

Floating point exception

[aquaskyline]

Using -g with only one copy of GRCh38.fa also work.

[sjackman]

Using -g rather than -r avoids running SURVIVOR and gets further:

simulateLinkedReads.pl -z 16 -x 524 -d 1 -1 0 -4 0 -7 0 -0 0 -g GRCh38.fa,GRCh38.fa -p sim.lr

[sjackman]

Also relevant is this commit 8abd7c1

added option n to disable all SVs

[sinamajidian]

Hi
I run this
~/Install/LRSIM/simulateLinkedReads.pl -r soltub_40.fasta -p out

The output is

Fri Dec 21 12:57:18 2018: out.status
Fri Dec 21 12:57:18 2018: Variant simulation mode enabled
Fri Dec 21 12:57:18 2018: SURVIVOR start
Fri Dec 21 12:57:18 2018: Running: /home/majid001/Install/LRSIM/SURVIVOR 0 soltub_40.fasta out.hap.parameter 0 out.hap 1000
Floating point exception
Fri Dec 21 12:57:18 2018: SURVIVOR error on missing out.hapA.fasta
No such file or directory at /home/majid001/Install/LRSIM/simulateLinkedReads.pl line 748.
unable to delete out.hapA.fasta at exit
unable to delete out.hap.hetB.insertions.fa at exit
unable to delete out.hap.homAB.insertions.fa at exit
unable to delete out.hap.hetA.insertions.fa at exit
unable to delete out.hapB.fasta at exit

In my pipeline, firstly, I should generate two haplotypes from the reference genome, then, generate some reads. Any idea?
I think using -g is not a good idea for my case. Because, haplotypes will not be created.