raid 0 vs raid 10

RAID level Sequential Reads (MB/s) Sequential Writes (MB/s) Random Reads (IOPS) Random Writes (IOPS)
RAID 0 Best Best Best Best
RAID 10 Better Better Best Better


One Liners


Report LGC

indel detection


test mpileup
./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup MM140738JS.bam -v -u > test.vcf

samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam

./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup -uf /lgc/datasets/hg19/new/hg19/hg19.fa MM140738JS.bam | ./samtools-bcftools-htslib-1.0_x64-linux/bin/bcftools call -mv > var.raw.vcf


python /lgc/scripts/ -i MM140738JS.bam -t /lgc/datasets/sickkids/AmpliSeqExome.20131001.designed.bed -o MM140738JS.indel.vcf

grep “72358746” *.vcf [ 7:47AM]
raony@mendel{MM140738JS} grep “72358745” *.vcf [ 7:48AM]
MM140738JS.indel.vcf:chr10 72358745 . CA C 1049.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.769;DP=84;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=81.36;MQ0=0;MQRankSum=-1.613;QD=12.50;ReadPosRankSum=0.095 GT:AD:DP:GQ:PL 0/1:47,32:81:99:1087,0,1785



$ sudo apt-add-repository ppa:neon/kf5
$ sudo apt-get update
$ sudo apt-get install project-neon5-session project-neon5-utils project-neon5-konsole

On startup

raony@einstein ~ $ free -m
total used free shared buffers cached
Mem: 3680 1659 2020 16 155 673
-/+ buffers/cache: 831 2849
Swap: 19072 0 19072

After opening Chrome

raony@einstein ~ $ free -m
total used free shared buffers cached
Mem: 3680 2684 995 26 180 863
-/+ buffers/cache: 1640 2040
Swap: 19072 0 19072



Fixing Python 3.4 in Ubuntu Trusty 14.04

Python 3.4 is broken in the new version of Ubuntu 14.04! (Which is a shame and should now happen! 😛 )

When you try to create a new virtual environment with “pyvenv venv” you get the following message:

pyvenv-3.4 test
Error: Command '['/home/raony/development/test_py3/test/bin/python3.4', '-Im', 'ensurepip', '--upgrade', '--default-pip']' returned non-zero exit status 1

I think this is because ensurepip is not included with python in the new version of Ubuntu 14.04 trusty.

You can read the discussion about this bug in here:

So for me the solution was to install two ssl-packages and python3.4 from source with the following commands:

sudo apt-get install libssl-dev openssl
tar -zxvf Python-3.4.0.tgz
cd Python-3.4.0
sudo make install

And them you can finally start creating your virtual environments again with the new venv module that comes with python 3.4 ( ! 🙂

pyvenv venv
source venv/bin/activate
pip install -r requirements.txt

And now I can finally start migrating my django projects from python 2.7 to python 3.4! Uhuuu!