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.dir_bash_history
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#1475862008
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1475862008
cd /media/thor/storage/rb_pipeline/
#1475862008
ls
#1475862014
history -a
#1475862022
echo history -a
#1475862033
ls
#1475862037
echo history -a
#1475862113
source ~/.bashrc
#1475862120
ls
#1475862133
history -a
#1475862133
history -a
#1475862156
thor has exited /media/thor/storage/rb_pipeline for
#1475862206
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1475862206
cd /media/thor/storage/rb_pipeline/
#1475862207
ls
#1475862216
history
#1475862372
thor has exited /media/thor/storage/rb_pipeline for ../kooi_rb_pipeline/
#1475869698
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1475869698
cd /media/thor/storage/rb_pipeline/
#1475869699
ls
#1475869791
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta indelrealigner
#1476042992
ls
#1476042995
thor has exited /media/thor/storage/rb_pipeline for gatk/
#1476131379
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476131379
cd /media/thor/storage/rb_pipeline/
#1476131381
ls
#1476131492
thor has exited /media/thor/storage/rb_pipeline for ..
#1476207709
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476207709
cd /media/thor/storage/rb_pipeline/
#1476207710
ls
#1476215260
thor has entered /media/thor/storage/rb_pipeline from /media/sf_vm_share/EgaDemoClient
#1476215260
cd /media/thor/storage/rb_pipeline/
#1476215260
ls
#1476215297
ls -lh
#1476216826
scp ucsc.hg19.* [email protected]:~/IRSAN
#1476220201
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476220201
cd /media/thor/storage/rb_pipeline/
#1476220202
ls
#1476220300
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta baserecalibrator
#1476222545
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476222545
cd /media/thor/storage/rb_pipeline/
#1476222608
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476224886
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta recal_bamindex
#1476225082
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476222413
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta printreads
#1476290300
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476290300
cd /media/thor/storage/rb_pipeline/
#1476290300
ls
#1476290348
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta variantfiltration
#1476290456
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta annovar
#1476299038
thor has entered /media/thor/storage/rb_pipeline from /home/thor/TOOLS
#1476299038
cd /media/thor/storage/rb_pipeline/
#1476299038
ls
#1476299047
vi rb_pipeline.py
#1476301732
ls
#1476301771
thor has exited /media/thor/storage/rb_pipeline for ..
#1476301844
thor has entered /media/thor/storage/rb_pipeline from /usr/share/perl/5.22.1/annovar
#1476301844
cd /media/thor/storage/rb_pipeline/
#1476301844
ls
#1476301908
/usr/share/perl/5.22.1/annovar/table_annovar.pl -downdb -webfrom annovar -buildver hg19 dbnsfp30a humandb/
#1476301978
sudo /usr/share/perl/5.22.1/annovar/table_annovar.pl -downdb -webfrom annovar -buildver hg19 dbnsfp30a humandb/
#1476302025
thor has exited /media/thor/storage/rb_pipeline for /usr/share/perl/5.22.1/annovar
#1476302088
thor has entered /media/thor/storage/rb_pipeline from /usr/share/perl/5.22.1/annovar
#1476302088
cd /media/thor/storage/rb_pipeline/
#1476302089
ls
#1476302092
thor has exited /media/thor/storage/rb_pipeline for humandb/
#1476302122
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/rb_pipeline/humandb
#1476302122
cd ..
#1476302123
ls
#1476302125
thor has exited /media/thor/storage/rb_pipeline for ..
#1476302388
thor has entered /media/thor/storage/rb_pipeline from /home/thor/TOOLS
#1476302388
cd /media/thor/storage/rb_pipeline/
#1476302388
ls
#1476302439
perl usr/share/perl/5.22.1/annovar/annotate_variation.pl -downdb -webfrom annovar -buildver hg19 dbnsfp30a humandb/
#1476302538
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476302538
cd /media/thor/storage/rb_pipeline/
#1476302539
ls
#1476302457
perl /usr/share/perl/5.22.1/annovar/annotate_variation.pl -downdb -webfrom annovar -buildver hg19 dbnsfp30a humandb/
#1476303091
thor has exited /media/thor/storage/rb_pipeline for ../..
#1476288814
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta baserecalibrator
#1476302543
vi rb_pipeline.py
#1476306174
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage
#1476306174
cd rb_pipeline/
#1476306175
ls
#1476306208
cat rb_pipeline.py
#1476306306
./rb_pipeline.py /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476306313
vi rb_pipeline.py
#1476306387
./rb_pipeline.py /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476306417
vi rb_pipeline.py
#1476306441
./rb_pipeline.py /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476306861
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476310653
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage
#1476310653
cd rb_pipeline/
#1476310654
ls
#1476314617
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476314617
cd /media/thor/storage/rb_pipeline/
#1476314618
ls
#1476314980
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta annovar
#1476315772
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476315772
cd /media/thor/storage/rb_pipeline/
#1476315773
ls
#1476315872
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476315872
cd /media/thor/storage/rb_pipeline/
#1476315873
ls
#1476315794
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta printreads
#1476310684
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta printreads
#1476316856
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476316856
cd /media/thor/storage/rb_pipeline/
#1476316874
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta annovar
#1476318063
perl usr/share/perl/5.22.1/annovar/table_annovar.pl /home/thor/rb_output/annovar/46-CL_1.avinput /media/thor/storage/humandb/ -protocol dbnsfp30a -operation f -build hg19 -nastring .
#1476318088
perl /usr/share/perl/5.22.1/annovar/table_annovar.pl /home/thor/rb_output/annovar/46-CL_1.avinput /media/thor/storage/humandb/ -protocol dbnsfp30a -operation f -build hg19 -nastring .
#1476318135
perl /usr/share/perl/5.22.1/annovar/table_annovar.pl /home/thor/rb_output/annovar/46-CL_1.avinput /media/thor/storage/rb_pipeline/humandb/ -protocol dbnsfp30a -operation f -build hg19 -nastring .
#1476375216
perl /usr/share/perl/5.22.1/annovar/variants_reduction.pl /home/thor/rb_output/annovar/46-CL_1.avinput /media/thor/storage/rb_pipeline/humandb/ -protocol nonsyn_splicing,genomicSuperDups,phastConsElements46way,1000g2014oct_all,esp6500siv2_ea,esp6500siv2_aa,snp135NonFlagged,dominant -operation g,rr,r,f,f,f,f,m -out reduce -buildver hg19
#1476375448
perl /usr/share/perl/5.22.1/annovar/table_annovar.pl /home/thor/rb_output/annovar/46-CL_1.avinput /media/thor/storage/rb_pipeline/humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp138,ljb23_all -operation g,r,r,f,f,f,f -nastring .
#1476375956
thor has entered /media/thor/storage/rb_pipeline from /usr/share/perl/5.22.1
#1476375956
cd /media/thor/storage/rb_pipeline/
#1476375957
ls
#1476379304
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476379304
cd /media/thor/storage/rb_pipeline/
#1476379304
ls
#1476379325
thor has exited /media/thor/storage/rb_pipeline for /home
#1476316678
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta baserecalibrator
#1476469438
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476469438
cd /media/thor/storage/rb_pipeline/
#1476469455
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta annovar
#1476479854
thor has exited /media/thor/storage/rb_pipeline for ../../../..
#1476481076
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476481076
cd /media/thor/storage/rb_pipeline/
#1476481077
ls
#1476481082
thor has exited /media/thor/storage/rb_pipeline for tabix-0.2.6/
#1476483941
/media/thor/storage/rb_pipeline/
#1476483942
ls
#1476483905
htop
#1476483969
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta printreads
#1476315899
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476719900
thor has exited /media/thor/storage/rb_pipeline for ../kooi_rb_pipeline/
#1476719486
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta baserecalibrator
#1476829530
htop
#1476811951
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta printreads
#1476899417
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476899417
cd /media/thor/storage/rb_pipeline/
#1476899418
ls
#1476899438
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476900413
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1476900413
cd /media/thor/storage/rb_pipeline/
#1476900759
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage
#1476900759
cd rb_pipeline/
#1476900760
ls
#1476900769
thor has exited /media/thor/storage/rb_pipeline for ..
#1476903756
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/rb_pipeline/bwa
#1476903756
cd ..
#1476903777
cp bwa CopywriteR
#1476903779
ls
#1476903799
thor has exited /media/thor/storage/rb_pipeline for /media/thor/storage/rb_pipeline/
#1476903799
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/rb_pipeline
#1476903799
cd /media/thor/storage/rb_pipeline/
#1476903800
ls
#1476904145
thor has exited /media/thor/storage/rb_pipeline for picard/
#1476998629
thor has entered /media/thor/storage/rb_pipeline from /
#1476998628
cd /media/thor/storage/rb_pipeline/
#1476998629
ls
#1476998636
thor has exited /media/thor/storage/rb_pipeline for picard/
#1476996600
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1476900433
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta printreads
#1477096181
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta printreads >printreads.out 2>&1 &
#1477096244
thor has entered /media/thor/storage/rb_pipeline from /home/thor/rb_output/picard/output
#1477096244
cd /media/thor/storage/rb_pipeline/
#1477096245
ls
#1477096336
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2 >mutect2.out 2>&1 &
#1477240373
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477240373
cd /media/thor/storage/rb_pipeline/
#1477240374
ls
#1477240388
cat mutect2.out
#1477240399
ls
#1477240408
cat printreads.out
#1477240420
htop
#1477240444
thor has exited /media/thor/storage/rb_pipeline for picard/
#1477240766
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/rb_pipeline/picard/CNAprofiles
#1477240766
cd ../..
#1477240767
ls
#1477240769
thor has exited /media/thor/storage/rb_pipeline for ..
#1477342578
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/rb_pipeline/picard
#1477342578
cd ..
#1477342582
ls
#1477342592
cat printreads.out
#1477342596
ls
#1477342602
cat mutect2.out
#1477342606
ls
#1477342612
thor has exited /media/thor/storage/rb_pipeline for ../kooi_rb_pipeline/
#1477364759
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/kooi_rb_pipeline
#1477364759
cd ../rb_pipeline/
#1477364760
ls
#1477364763
thor has exited /media/thor/storage/rb_pipeline for picard/
#1477414042
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage
#1477414042
cd rb_pipeline/
#1477414045
ls
#1477414056
cat mutect2.out
#1477414203
thor has exited /media/thor/storage/rb_pipeline for ..
#1477096341
htop
#1477326828
htop
#1477416853
thor has entered /media/thor/storage/rb_pipeline from /usr/share/java
#1477416853
cd /media/thor/storage/rb_pipeline/
#1477416854
ls
#1477417802
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect
#1477417839
thor has exited /media/thor/storage/rb_pipeline for /usr/share/java
#1477417864
thor has entered /media/thor/storage/rb_pipeline from /usr/share/java
#1477417864
cd /media/thor/storage/rb_pipeline/
#1477417908
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect
#1477417950
screen -ls
#1477417960
screen -r 4226
#1477417758
screen
#1477417987
screen -x
#1477418001
screen -x 4226
#1477418004
ls
#1477418060
screen -dr
#1477418069
screen -dr 4226
#1477418138
screen -xR 4226
#1477418140
ls
#1477418145
screen
#1477417977
screen -r 4226
#1477418162
exit
#1477418153
screen
#1477418166
screen -ls
#1477418200
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect
#1477418575
screen -r
#1477418177
screen -r 4226
#1477418596
screen -r 3588
#1477418611
screen -r 31989
#1477418868
screen -r 4266
#1477418874
screen -ls
#1477418904
exit
#1477418883
screen -r 4226
#1477419132
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect
#1477419173
exit
#1477419186
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect
#1477419282
thor has exited /media/thor/storage/rb_pipeline for /usr/share/java
#1477419495
thor has entered /media/thor/storage/rb_pipeline from /usr/share/java
#1477419495
cd /media/thor/storage/rb_pipeline/
#1477419507
java -jar /usr/share/java/muTect-1.1.4.jar --analysis_type MuTect --reference_sequence ucsc.hg19.fasta --dbsnp /media/thor/storage/rb_pipeline/dbsnp_138.hg19.excluding_sites_after_129.vcf --intervals /media/thor/storage/rb_pipeline/agilent_targets_hg19.interval_list --input_file:normal /home/thor/rb_output/gatk/41-N_1_recalibrated.bam --input_file:tumor /home/thor/rb_output/gatk/41-T_1_recalibrated.bam --out /home/thor/rb_output/gatk/mutect/41-T_1_mutect.vcf --coverage_file /home/thor/rb_output/gatk/mutect/41-T_1_mutect_coverage.wig.txt
#1477420036
java -version
#1477420223
sudo update-alternatives --config java
#1477420479
sudo add-apt-repository ppa:webupd8team/java
#1477420524
aduo apt-get update
#1477420530
sudo apt-get update
#1477420561
sudo apt-get install oracle-java7-installer
#1477420714
java -jar /usr/share/java/muTect-1.1.4.jar --analysis_type MuTect --reference_sequence ucsc.hg19.fasta --dbsnp /media/thor/storage/rb_pipeline/dbsnp_138.hg19.excluding_sites_after_129.vcf --intervals /media/thor/storage/rb_pipeline/agilent_targets_hg19.interval_list --input_file:normal /home/thor/rb_output/gatk/41-N_1_recalibrated.bam --input_file:tumor /home/thor/rb_output/gatk/41-T_1_recalibrated.bam --out /home/thor/rb_output/gatk/mutect/41-T_1_mutect.vcf --coverage_file /home/thor/rb_output/gatk/mutect/41-T_1_mutect_coverage.wig.txt
#1477426400
screen -r
#1477426414
d
#1477426438
exit
#1477426421
screen
#1477428468
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477428468
cd /media/thor/storage/rb_pipeline/
#1477428469
l
#1477428474
ls
#1477428954
sudo update-alternatives --config java
#1477495083
htop
#1477495108
thor has exited /media/thor/storage/rb_pipeline for /media/thor/storage/rb_pipeline/
#1477495108
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/rb_pipeline
#1477495108
cd /media/thor/storage/rb_pipeline/
#1477495109
ls
#1477495185
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2
#1477495458
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage/rb_pipeline/picard
#1477495458
cd /media/thor/storage/rb_pipeline/
#1477495492
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2 &
#1477429227
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta haplotypecaller
#1477688546
ls
#1477688559
cat nohup.out
#1477688607
hotp
#1477688638
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta mutect2 &
#1477689816
ifconfig
#1477689820
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477689820
cd /media/thor/storage/rb_pipeline/
#1477689821
ls
#1477688610
htop
#1477692886
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta baserecalibrator &
#1477693680
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477693680
cd /media/thor/storage/rb_pipeline/
#1477693681
ls
#1477693689
vi run_gistic_cobrinik_rb
#1477698515
cat nohup.out
#1477701621
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477701621
cd /media/thor/storage/rb_pipeline/
#1477701637
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta bwa-aligner
#1477701873
bwa mem -M -t 6 -R @RGID:H7TKWBBXX_3_1101SM:43-CL_1PL:Illumina ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz
#1477701998
bwa mem -M -t 6 -R @RGID:H7TKWBBXX_3_1101\tSM:43-CL_1\tPL:Illumina ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz
#1477702070
bwa mem -M -t 6 -R @RG\tID:H7TKWBBXX_3_1101\tSM:43-CL_1\tPL:Illumina ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz
#1477702112
bwa mem -M -t 6 -R "@RG\tID:H7TKWBBXX_3_1101\tSM:43-CL_1\tPL:Illumina" ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz
#1477702297
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477702297
cd /media/thor/storage/rb_pipeline/
#1477702421
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta collecthsmetrics >collecthsmetrics.out >2&1
#1477702474
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta collecthsmetrics
#1477702770
nohup ./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta collecthsmetrics >collecthsmetrics.out >2&1
#1477702864
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477702864
cd /media/thor/storage/rb_pipeline/
#1477702920
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta collectinsersizemetrics
#1477702932
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta collectinsertsizemetrics
#1477702988
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta collectismetrics
#1477702777
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta collecthsmetrics
#1477932900
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477932900
cd /media/thor/storage/rb_pipeline/
#1477932900
ls
#1477932929
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta sortsam
#1477933172
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477933172
cd /media/thor/storage/rb_pipeline/
#1477933194
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta baserecalibrator
#1477933222
java -jar /usr/share/java/GenomeAnalysisTK.jar -T BaseRecalibrator -R ucsc.hg19.fasta -I /home/thor/rb_output/picard/markduplicates/48-N_1_marked_duplicates.bam -knownSites /media/thor/storage/rb_pipeline/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -knownSites /media/thor/storage/rb_pipeline/1000G_phase1.indels.hg19.sites.vcf -knownSites /media/thor/storage/rb_pipeline/dbsnp_138.hg19.excluding_sites_after_129.vcf -o /home/thor/rb_output/gatk/48-N_1_recal_report.table -rf BadCigar
#1477933293
java -jar /usr/share/java/GenomeAnalysisTK.jar -T BaseRecalibrator -R ucsc.hg19.fasta -I /home/thor/rb_output/picard/markduplicates/20-N_1_marked_duplicates.bam -knownSites /media/thor/storage/rb_pipeline/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -knownSites /media/thor/storage/rb_pipeline/1000G_phase1.indels.hg19.sites.vcf -knownSites /media/thor/storage/rb_pipeline/dbsnp_138.hg19.excluding_sites_after_129.vcf -o /home/thor/rb_output/gatk/20-N_1_recal_report.table -rf BadCigar
#1477933029
java -jar /usr/share/java/picard.jar SortSam I= /home/thor/storage/rb_pipeline/picard/43-CL_1.bam O= /home/thor/rb_output/picard/43-CL_1_sorted.bam SORT_ORDER=coordinate
#1477933842
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta bwa-aligner
#1477933927
bwa mem -M -t 6 -R @RGID:H7TKWBBXX_3_1101SM:43-CL_1PL:Illumina ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz
#1477933957
bwa mem -M -t 6 -R @RG\tID:H7TKWBBXX_3_1101\tSM:43-CL_1\tPL:Illumina ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz
#1477933979
bwa mem -M -t 6 -R "@RG\tID:H7TKWBBXX_3_1101\tSM:43-CL_1\tPL:Illumina" ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz
#1477933348
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta buildbamindex
#1477934279
bwa mem -M -t 6 -R "@RG\tID:H7TKWBBXX_3_1101\tSM:43-CL_1\tPL:Illumina" ucsc.hg19.fasta /media/sf_RB_exome_project/43-CL_1.fastq.gz /media/sf_RB_exome_project/43-CL_2.fastq.gz > /home/thor/rb_output/bwa/43-CL_1.sam
#1477944267
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477944267
cd /media/thor/storage/rb_pipeline/
#1477944310
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta haplotypecaller
#1477944321
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta haplocaller
#1477945435
thor has entered /media/thor/storage/rb_pipeline from /home/thor
#1477945435
cd /media/thor/storage/rb_pipeline/
#1477945437
thor has exited /media/thor/storage/rb_pipeline for picard/
#1477944214
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta samformatconverter
#1477944162
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta baserecalibrator
#1477944584
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta haplotypecaller
#1478020756
./run_rb_pipeline.sh /media/sf_RB_exome_project/ ucsc.hg19.fasta sortsam
#1478020790
./run_rb_pipeline.sh /media/thor/storage/rb_pipeline/ ucsc.hg19.fasta sortsam
#1478021003
java -jar /usr/share/java/picard.jar SortSam I= /home/thor/rb_output/picard/193-CL_1.bam O= /home/thor/rb_output/picard/193-CL_1_sorted.bam SORT_ORDER=coordinate
#1478021031
java -jar /usr/share/java/picard.jar SortSam I= /home/thor/rb_output/picard/43-CL_1.bam O= /home/thor/rb_output/picard/43-CL_1_sorted.bam SORT_ORDER=coordinate
#1478034604
./run_rb_pipeline.sh /media/thor/storage/rb_pipeline/ ucsc.hg19.fasta markduplicates
#1478034675
java -jar /usr/share/java/picard.jar MarkDuplicates I= /home/thor/rb_output/picard/43-CL_1_sorted.bam O= /home/thor/rb_output/picard/markduplicates/43-CL_1_marked_duplicates.bam M= /home/thor/rb_output/picard/43-CL_1_marked_dup_metrics.txt TMP_DIR= /home/thor/rb_output/picard/tmp/
#1478047783
diff ./picard/ /home/thor/rb_output/picard/
#1478047855
diff ./picard/ /home/thor/rb_output/picard/ > picard_diff_11012016.txt
#1478047928
ls
#1478047930
thor has exited /media/thor/storage/rb_pipeline for ..
#1478048587
diff /media/sf_RB_exome_project/ /media/thor/storage/rb_pipeline/ > fastq_source_diff_11012016.txt
#1478049070
diff /media/sf_RB_exome_project/ /media/thor/storage/rb_pipeline/ -x *.fastq.gz > fastq_source_diff_11012016.txt
#1478049084
diff /media/sf_RB_exome_project/ /media/thor/storage/rb_pipeline/ *.fastq.gz > fastq_source_diff_11012016.txt
#1478049121
diff /media/sf_RB_exome_project/ /media/thor/storage/rb_pipeline/ -x "*.fastq.gz" > fastq_source_diff_11012016.txt
#1478049256
find . -type f -not -name '*.fastq.gz' | xargs -I% basename '%' | awk -F . 'NF > 1 { print "*." $NF}; NF == 1 { print $NF }' | sort | uniq > exclude.pats
#1478049296
diff /media/sf_RB_exome_project/ /media/thor/storage/rb_pipeline/ -X exclude.pats > fastq_source_diff_11012016.txt
#1478049311
cat fastq_source_diff_11012016.txt
#1478049324
ls
#1478049547
./run_rb_pipeline.sh /media/thor/storage/rb_pipeline/ ucsc.hg19.fasta markduplicates
#1478049844
./run_rb_pipeline.sh /media/thor/storage/rb_pipeline/ ucsc.hg19.fasta sortsam
#1478050185
thor has entered /media/thor/storage/rb_pipeline from /media/thor/storage
#1478050185
cd /media/thor/storage/rb_pipeline/
#1478050202
./run_rb_pipeline.sh /media/thor/storage/rb_pipeline/ ucsc.hg19.fasta markduplicates
#1478108546
thor has exited /media/thor/storage/rb_pipeline for ../../..
#1478112249
thor has entered /media/thor/storage/rb_pipeline from /home/thor/TOOLS
#1478112249
cd /media/thor/storage/rb_pipeline/
#1478112250
ls
#1478112420
./run_rb_pipeline.sh /media/thor/storage/rb_pipeline/ ucsc.hg19.fasta genotypegvcfs
#1478113140
cat fastq_source_diff_11012016.txt
#1478113146
./run_rb_pipeline.sh /media/thor/storage/rb_pipeline/ ucsc.hg19.fasta genotypegvcfs
#1478112260
vi rb_pipeline.py