User:Lindenb/Notebook/UMR915/20110615: Difference between revisions

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"AX-11086611","rs10001340","4","130341127","+","0","q28.2","[A/C]agggcattcatctcagcttactatttgggaaaaat","A","C","ENST00000281146 // downstream // 306645 // Hs.567679 // C4orf33 // 132321 // chromosome 4 open reading frame 33 /// ENST00000394248 // upstream // 3729342 // Hs.192859 // PCDH10 // 57575 // protocadherin 10 /// NM_173487 // downstream // 307285 // Hs.567679 // C4orf33 // 132321 // chromosome 4 open reading frame 33 /// NM_020815 // upstream // 3729342 // Hs.192859 // PCDH10 // 57575 // protocadherin 10","127.864057946266 // D4S1615 // D4S2365 // --- // --- /// 129.756132396152 // D4S2938 // D4S2365 // AFMA284WG5 // GATA10A12 /// 124.03426335901 // D4S2394 // --- // --- // 55218","D4S3198 // upstream // 331274 /// D4S2394 // downstream // 43310","0.815789474 // 0.184210526 // Caucasian /// 1.0 // 0.0 // Han Chinese /// 1.0 // 0.0 // Japanese /// 0.816666667 // 0.183333333 // Yoruban","0.368421053 // Caucasian /// 0.0 // Han Chinese /// 0.0 // Japanese /// 0.266666667 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","C // Caucasian /// C // Han Chinese /// C // Japanese /// C // Yoruban","0.184210526 // Caucasian /// 0.0 // Han Chinese /// 0.0 // Japanese /// 0.183333333 // Yoruban","---"
"AX-11086611","rs10001340","4","130341127","+","0","q28.2","[A/C]agggcattcatctcagcttactatttgggaaaaat","A","C","ENST00000281146 // downstream // 306645 // Hs.567679 // C4orf33 // 132321 // chromosome 4 open reading frame 33 /// ENST00000394248 // upstream // 3729342 // Hs.192859 // PCDH10 // 57575 // protocadherin 10 /// NM_173487 // downstream // 307285 // Hs.567679 // C4orf33 // 132321 // chromosome 4 open reading frame 33 /// NM_020815 // upstream // 3729342 // Hs.192859 // PCDH10 // 57575 // protocadherin 10","127.864057946266 // D4S1615 // D4S2365 // --- // --- /// 129.756132396152 // D4S2938 // D4S2365 // AFMA284WG5 // GATA10A12 /// 124.03426335901 // D4S2394 // --- // --- // 55218","D4S3198 // upstream // 331274 /// D4S2394 // downstream // 43310","0.815789474 // 0.184210526 // Caucasian /// 1.0 // 0.0 // Han Chinese /// 1.0 // 0.0 // Japanese /// 0.816666667 // 0.183333333 // Yoruban","0.368421053 // Caucasian /// 0.0 // Han Chinese /// 0.0 // Japanese /// 0.266666667 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","C // Caucasian /// C // Han Chinese /// C // Japanese /// C // Yoruban","0.184210526 // Caucasian /// 0.0 // Han Chinese /// 0.0 // Japanese /// 0.183333333 // Yoruban","---"
"AX-11086610","rs10001337","4","54351529","+","0","q12","atgaggagtagccacatgatctaagcacct[C/T]","T","C","ENST00000306888 // --- // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// ENST00000263925 // --- // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// NM_001126328 // intron // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// NM_032622 // intron // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1","67.4182086016315 // D4S2971 // D4S1594 // --- // --- /// 62.2091955728879 // D4S2971 // UNKNOWN // AFMB312YG1 // GATA61B02 /// 61.6059658777947 // --- // GATA61B02 // 149925 // ---","D4S461 // upstream // 151923 /// D4S2583E // downstream // 24481","0.118644068 // 0.881355932 // Caucasian /// 0.111111111 // 0.888888889 // Han Chinese /// 0.122222222 // 0.877777778 // Japanese /// 0.025 // 0.975 // Yoruban","0.203389831 // Caucasian /// 0.133333333 // Han Chinese /// 0.244444444 // Japanese /// 0.05 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","T // Caucasian /// T // Han Chinese /// T // Japanese /// T // Yoruban","0.118644068 // Caucasian /// 0.111111111 // Han Chinese /// 0.122222222 // Japanese /// 0.025 // Yoruban","---"</pre>
"AX-11086610","rs10001337","4","54351529","+","0","q12","atgaggagtagccacatgatctaagcacct[C/T]","T","C","ENST00000306888 // --- // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// ENST00000263925 // --- // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// NM_001126328 // intron // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// NM_032622 // intron // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1","67.4182086016315 // D4S2971 // D4S1594 // --- // --- /// 62.2091955728879 // D4S2971 // UNKNOWN // AFMB312YG1 // GATA61B02 /// 61.6059658777947 // --- // GATA61B02 // 149925 // ---","D4S461 // upstream // 151923 /// D4S2583E // downstream // 24481","0.118644068 // 0.881355932 // Caucasian /// 0.111111111 // 0.888888889 // Han Chinese /// 0.122222222 // 0.877777778 // Japanese /// 0.025 // 0.975 // Yoruban","0.203389831 // Caucasian /// 0.133333333 // Han Chinese /// 0.244444444 // Japanese /// 0.05 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","T // Caucasian /// T // Han Chinese /// T // Japanese /// T // Yoruban","0.118644068 // Caucasian /// 0.111111111 // Han Chinese /// 0.122222222 // Japanese /// 0.025 // Yoruban","---"</pre>
=GeneTitan pictures=
[[Image:GeneTitan20110615a.jpg]]
[[Image:GeneTitan20110615b.jpg]]


===Calls===
===Calls===

Revision as of 08:25, 15 June 2011

20110614        Top        20110615       


hadoop

(started on User:Lindenb/Notebook/UMR915/20110610 }

trying to change /etc/hosts: https://twitter.com/#!/fredebibs/status/79170165312454656

then 

sudo /etc/rc.d/init.d/network restart

success ! 

[lindenb@srv-clc-04 hadoop-0.20.203.0]$  bin/hadoop namenode -format
11/06/15 08:32:13 INFO namenode.NameNode: STARTUP_MSG: 
/************************************************************
STARTUP_MSG: Starting NameNode
STARTUP_MSG:   host = srv-clc-04.u915.irt.univ-nantes.prive3/127.0.0.1
STARTUP_MSG:   args = [-format]
STARTUP_MSG:   version = 0.20.203.0
STARTUP_MSG:   build = http://svn.apache.org/repos/asf/hadoop/common/branches/branch-0.20-security-203 -r 1099333; compiled by 'oom' on Wed May  4 07:57:50 PDT 2011
************************************************************/
11/06/15 08:32:13 INFO util.GSet: VM type       = 64-bit
11/06/15 08:32:13 INFO util.GSet: 2% max memory = 19.1675 MB
11/06/15 08:32:13 INFO util.GSet: capacity      = 2^21 = 2097152 entries
11/06/15 08:32:13 INFO util.GSet: recommended=2097152, actual=2097152
11/06/15 08:32:13 INFO namenode.FSNamesystem: fsOwner=lindenb
11/06/15 08:32:13 INFO namenode.FSNamesystem: supergroup=supergroup
11/06/15 08:32:13 INFO namenode.FSNamesystem: isPermissionEnabled=true
11/06/15 08:32:13 INFO namenode.FSNamesystem: dfs.block.invalidate.limit=100
11/06/15 08:32:13 INFO namenode.FSNamesystem: isAccessTokenEnabled=false accessKeyUpdateInterval=0 min(s), accessTokenLifetime=0 min(s)
11/06/15 08:32:13 INFO namenode.NameNode: Caching file names occuring more than 10 times 
11/06/15 08:32:13 INFO common.Storage: Image file of size 113 saved in 0 seconds.
11/06/15 08:32:14 INFO common.Storage: Storage directory /home/lindenb/tmp/HADOOP/dfs/name has been successfully formatted.
11/06/15 08:32:14 INFO namenode.NameNode: SHUTDOWN_MSG: 
/************************************************************
SHUTDOWN_MSG: Shutting down NameNode at srv-clc-04.u915.irt.univ-nantes.prive3/127.0.0.1

start the server

[lindenb@srv-clc-04 hadoop-0.20.203.0]$ ./bin/start-all.sh 
namenode running as process 1151. Stop it first.
localhost: starting datanode, logging to /home/lindenb/package/hadoop-0.20.203.0/bin/../logs/hadoop-lindenb-datanode-srv-clc-04.u915.irt.univ-nantes.prive3.out
localhost: secondarynamenode running as process 1490. Stop it first.
jobtracker running as process 1588. Stop it first.
localhost: starting tasktracker, logging to /home/lindenb/package/hadoop-0.20.203.0/bin/../logs/hadoop-lindenb-tasktracker-srv-clc-04.u915.irt.univ-nantes.prive3.out

copy cDINA data

bin/hadoop fs  -mkdir myfolder
fs -copyFromLocal ~/Axiom_GW_Hu_SNP.r2.na31.annot.csv myfolder/


bin/hadoop fs -tail /user/lindenb/myfolder/Axiom_GW_Hu_SNP.r2.na31.annot.csv
s.135270 // CRMP1 // 1400 // collapsin response mediator protein 1 /// NM_001099433 // downstream // 100570 // Hs.479066 // JAKMIP1 // 152789 // janus kinase and microtubule interacting protein 1","10.7510808767857 // D4S2925 // D4S2366 // --- // --- /// 11.4380209151363 // D4S2285 // D4S431 // UT5936 // AFM262VG9 /// 10.964419629995 // --- // D4S2366 // 58988 // ---","D4S1059 // upstream // 121041 /// D4S2509E // downstream // 104845","0.108333333 // 0.891666667 // Caucasian /// 0.055555556 // 0.944444444 // Han Chinese /// 0.011111111 // 0.988888889 // Japanese /// 0.041666667 // 0.958333333 // Yoruban","0.183333333 // Caucasian /// 0.066666667 // Han Chinese /// 0.022222222 // Japanese /// 0.083333333 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","T // Caucasian /// T // Han Chinese /// T // Japanese /// T // Yoruban","0.108333333 // Caucasian /// 0.055555556 // Han Chinese /// 0.011111111 // Japanese /// 0.041666667 // Yoruban","---"



#serveur1: scp  /CGH/data/users/cdina/DATAS/CEDRIC/Axiom2/resultat/AxiomGT1.calls.txt lindenb@serveur4:
bin/hadoop fs -copyFromLocal ~/AxiomGT1.calls.txt myfolder/


$ ls -lah ~/Axiom*
-rw-r--r-- 1 lindenb lindenb 111M jun 15 09:03 /home/lindenb/AxiomGT1.calls.txt
-rw-r--r-- 1 lindenb lindenb 766M jun 10 12:35 /home/lindenb/Axiom_GW_Hu_SNP.r2.na31.annot.csv

du -h ~/tmp/HADOOP | tail -1
884M	/home/lindenb/tmp/HADOOP

Files

Axiom_GW_Hu_SNP.r2.na31.annot.csv

"Probe Set ID","dbSNP RS ID","Chromosome","Physical Position","Strand","ChrX pseudo-autosomal region 1","Cytoband","Flank","Allele A","Allele B","Associated Gene","Genetic Map","Microsatellite","Allele Frequencies","Heterozygous Allele Frequencies","Number of individuals/Number of chromosomes","In Hapmap","Strand Versus dbSNP","Probe Count","ChrX pseudo-autosomal region 2","Minor Allele","Minor Allele Frequency","OMIM"
"AX-11086612","rs10001348","4","29912308","+","0","p15.1","gtattcagttgaacacaaatcagtgcatgt[A/G]","A","G","ENST00000467087 // downstream // 2885305 // Hs.724550 // STIM2 // 57620 // stromal interaction molecule 2 /// ENST00000361762 // upstream // 809728 // Hs.479439 // PCDH7 // 5099 // protocadherin 7 /// NM_001169117 // downstream // 2885305 // Hs.724550 // STIM2 // 57620 // stromal interaction molecule 2 /// NM_032456 // upstream // 809728 // Hs.724529 // PCDH7 // 5099 // protocadherin 7","50.0229786923511 // D4S418 // D4S2408 // --- // --- /// 44.2128449948474 // D4S2397 // D4S2430 // ATA27C07 // GCT6F03 /// 42.4637111703432 // --- // --- // 226002 // 46437","D4S333 // upstream // 47955 /// D4S605 // downstream // 97312","0.872881356 // 0.127118644 // Caucasian /// 0.833333333 // 0.166666667 // Han Chinese /// 0.777777778 // 0.222222222 // Japanese /// 0.775 // 0.225 // Yoruban","0.254237288 // Caucasian /// 0.288888889 // Han Chinese /// 0.355555556 // Japanese /// 0.35 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","G // Caucasian /// G // Han Chinese /// G // Japanese /// G // Yoruban","0.127118644 // Caucasian /// 0.166666667 // Han Chinese /// 0.222222222 // Japanese /// 0.225 // Yoruban","---"
"AX-11086611","rs10001340","4","130341127","+","0","q28.2","[A/C]agggcattcatctcagcttactatttgggaaaaat","A","C","ENST00000281146 // downstream // 306645 // Hs.567679 // C4orf33 // 132321 // chromosome 4 open reading frame 33 /// ENST00000394248 // upstream // 3729342 // Hs.192859 // PCDH10 // 57575 // protocadherin 10 /// NM_173487 // downstream // 307285 // Hs.567679 // C4orf33 // 132321 // chromosome 4 open reading frame 33 /// NM_020815 // upstream // 3729342 // Hs.192859 // PCDH10 // 57575 // protocadherin 10","127.864057946266 // D4S1615 // D4S2365 // --- // --- /// 129.756132396152 // D4S2938 // D4S2365 // AFMA284WG5 // GATA10A12 /// 124.03426335901 // D4S2394 // --- // --- // 55218","D4S3198 // upstream // 331274 /// D4S2394 // downstream // 43310","0.815789474 // 0.184210526 // Caucasian /// 1.0 // 0.0 // Han Chinese /// 1.0 // 0.0 // Japanese /// 0.816666667 // 0.183333333 // Yoruban","0.368421053 // Caucasian /// 0.0 // Han Chinese /// 0.0 // Japanese /// 0.266666667 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","C // Caucasian /// C // Han Chinese /// C // Japanese /// C // Yoruban","0.184210526 // Caucasian /// 0.0 // Han Chinese /// 0.0 // Japanese /// 0.183333333 // Yoruban","---"
"AX-11086610","rs10001337","4","54351529","+","0","q12","atgaggagtagccacatgatctaagcacct[C/T]","T","C","ENST00000306888 // --- // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// ENST00000263925 // --- // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// NM_001126328 // intron // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1 /// NM_032622 // intron // 0 // Hs.518760 // LNX1 // 84708 // ligand of numb-protein X 1","67.4182086016315 // D4S2971 // D4S1594 // --- // --- /// 62.2091955728879 // D4S2971 // UNKNOWN // AFMB312YG1 // GATA61B02 /// 61.6059658777947 // --- // GATA61B02 // 149925 // ---","D4S461 // upstream // 151923 /// D4S2583E // downstream // 24481","0.118644068 // 0.881355932 // Caucasian /// 0.111111111 // 0.888888889 // Han Chinese /// 0.122222222 // 0.877777778 // Japanese /// 0.025 // 0.975 // Yoruban","0.203389831 // Caucasian /// 0.133333333 // Han Chinese /// 0.244444444 // Japanese /// 0.05 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","T // Caucasian /// T // Han Chinese /// T // Japanese /// T // Yoruban","0.118644068 // Caucasian /// 0.111111111 // Han Chinese /// 0.122222222 // Japanese /// 0.025 // Yoruban","---"

GeneTitan pictures


Calls

probeset_id	A05.CEL	A06.CEL	A03.CEL	A04.CEL	A01.CEL	A10.CEL	A02.CEL	A11.CEL	A12.CEL	A09.CEL	A07.CEL	A08.CEL	B01.CEL	B02.CEL	B06.CEL	B03.CEL	B04.CEL	B05.CEL	B07.CEL	B08.CEL	B09.CEL	B10.CEL	C02.CEL	B11.CEL	B12.CEL	C01.CEL	C03.CEL	C04.CEL	C05.CEL	C06.CEL	C07.CEL	C08.CEL	C09.CEL	C10.CEL	C11.CEL	C12.CEL	D01.CEL	D02.CEL	D03.CEL	D04.CEL	D05.CEL	D06.CEL	D07.CEL	D08.CEL	D09.CEL	D10.CEL	D11.CEL	D12.CEL	E01.CEL	E02.CEL	E03.CEL	E04.CEL	E05.CEL	E06.CEL	E07.CEL	E08.CEL	E09.CEL	E10.CEL	E11.CEL	E12.CEL	F01.CEL	F02.CEL	F03.CEL	F04.CEL	F05.CEL	F06.CEL	F07.CEL	F08.CEL	H08.CEL	H07.CEL	G07.CEL	G08.CEL	H03.CEL	H04.CEL	H06.CEL	H05.CEL	G09.CEL	G10.CEL	H01.CEL	H02.CEL	G11.CEL	G12.CEL	G03.CEL	G04.CEL	H10.CEL	H09.CEL	F10.CEL	F09.CEL	G01.CEL	G02.CEL	F11.CEL	F12.CEL	G05.CEL	G06.CEL	H11.CEL	H12.CEL
AX-11086525	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	0	1	0	0	1	1	2	1	1	0	0	0	0	1	0	0	1	0	0	1	1	0	1	0	1	1	2	0	1	0	0	1	2	0	2
AX-11086526	2	1	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	1	2	2	2	2	2	2	2	2	2	2	2	1	2	2	0	2	2	2	1	1	1	2	2	2	2	2	2	2	2	2	1	1	1	2	1	2	1	2	2	0	2	1	2	2	1	2	2	2	2	1	2	2	2	2	2	1	2	1	1	2	2	1	2	2	2	2	2	2	2	2	2	1	2	2	2
AX-11086527	2	0	2	2	2	1	2	2	2	2	2	2	2	2	2	2	2	2	2	2	1	2	2	2	2	2	2	2	2	1	2	2	1	1	0	2	1	2	1	2	2	1	1	1	1	2	2	1	0	2	1	2	1	2	2	2	1	2	1	1	1	1	2	2	2	2	2	1	1	0	2	0	1	0	1	0	1	2	1	1	0	1	1	0	2	1	1	1	0	1	1	1	2	2	1	1

Join

AX-11086525	4	165621955	rs10000041	T T	T T	T T	T T	T T	T T	T T	T G	T T	T T	T T	T T	T T	T T	T T	T T	T T	T T	T T	T G	T G	T T	T T	T G	T T	T T	T T	T T	T T	T T	T T	T T	T T	T T	T T	T T	T T	T G	T T	T T	T G	T T	T G	T T	T T	T T	T T	T T	T T	T T	T T	T T	T T	T G	T T	T T	T T	T T	T G	T T	T G	T T	T G	T T	T T	T G	T G	G G	T G	T G	T T	T T	T T	T T	T G	T T	T T	T G	T T	T T	T G	T G	T T	T G	T T	T G	T G	G G	T T	T G	T T	T T	T G	G G	T T	G G
AX-11086526	4	5237152	rs10000042	C C	T C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	T C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	C C	T C	C C	C C	T T	C C	C C	C C	T C	T C	T C	C C	C C	C C	C C	C C	C C	C C	C C	C C	T C	T C	T C	C C	T C	C C	T C	C C	C C	T T	C C	T C	C C	C C	T C	C C	C C	C C	C C	T C	C C	C C	C C	C C	C C	T C	C C	T C	T C	C C	C C	T C	C C	C C	C C	C C	C C	C C	C C	C C	C C	T C	C C	C C	C C
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