27-Aug-2013 D2C1VACXX Rockman

[smondet]

RUNID=130830_SN911_0178_BD2C1VACXX

• [x] create Submission Sheet(s) and email
• [x] validate Submission Sheet(s)
• [ ] if needed, remove previous run directories on rabbot:/hiseq to make space
• [ ] if needed, remove previous run directories on bowery:/scratch to make space
• [x] transfer data gencore@bowery$ qsub -v DIR=$RUNID ~/bin/rsync.pbs
• [x] make tarball qsub -v DIR=$RUNID ~/bin/tar.pbs
• [x] backup tarball to sftp.bio qsub -v DIR=$RUNID ~/bin/sftp.bio-backup.pbs
• [x] validate Submission Sheet(s) again and remove edit permissions
• [x] import Submission Sheet(s) and register flowcell
• [x] demultiplex
• [x] fastx
• [x] review statistics
• [x] deliver
• [x] send emails

[smondet]

gencore@bowery-0-3:~ $ qsub -v DIR=130830_SN911_0178_BD2C1VACXX bin/rsync.pbs
2521179.crunch.local

PBS Job Id: 2521179.crunch.local
Job Name:   hiseq-rsync
Exec host:  compute-12-14/3
Execution terminated
Exit_status=0
resources_used.cput=02:00:47
resources_used.mem=259640kb
resources_used.vmem=613356kb
resources_used.walltime=20:32:56

[smondet]

 $ hitscore production b2f start -user sm4431 -bases-mask 'Y*,I8,I8,Y*' /scratch/gencore/hiseq-700911/130830_SN911_0178_BD2C1VACXX

Evaluation 31550 started.

FAILED

[smondet]

$ qsub -v DIR=130830_SN911_0178_BD2C1VACXX ~/bin/rsync.pbs 
2528903.crunch.local

PBS Job Id: 2528903.crunch.local
Job Name:   hiseq-rsync
Exec host:  compute-13-0/8
Execution terminated
Exit_status=0
resources_used.cput=01:17:35
resources_used.mem=259476kb
resources_used.vmem=613584kb
resources_used.walltime=33:30:29

[smondet]

 $ qsub -v DIR=130830_SN911_0178_BD2C1VACXX ~/bin/tar.pbs 
2541535.crunch.local

PBS Job Id: 2541535.crunch.local
Job Name:   tar
Exec host:  compute-13-25/2
Execution terminated
Exit_status=0
resources_used.cput=10:00:13
resources_used.mem=5332kb
resources_used.vmem=216216kb
resources_used.walltime=42:01:11

[smondet]

hitscore production b2f start -user sm4431 D2C1VACXX -bases-mask Y*,I8,I8,Y*

Evaluation 31815 started.

[smondet]

 $ hitscore production fxqs start -user sm4431 -from-b2f 31815 
aa144 : cgsb users
sm4431 : cgsb users
ps103 : cgsb users carlton
id: jsd6: No such user
kw1213 : cgsb users
carltj01 : cgsb users carlton
aa144 : cgsb users
sm4431 : cgsb users
ps103 : cgsb users carlton
id: jsd6: No such user
kw1213 : cgsb users
carltj01 : cgsb users carlton
aa144 : cgsb users
sm4431 : cgsb users
ps103 : cgsb users carlton
id: jsd6: No such user
kw1213 : cgsb users
carltj01 : cgsb users carlton
aa144 : cgsb users
sm4431 : cgsb users
ps103 : cgsb users carlton
id: jsd6: No such user
kw1213 : cgsb users
carltj01 : cgsb users carlton
aa144 : cgsb users
sm4431 : cgsb users
ps103 : cgsb users carlton
id: jsd6: No such user
kw1213 : cgsb users
carltj01 : cgsb users carlton
Creating VFS link (coerce_b2f_unaligned)
Evaluation 31852 started!

[smondet]

 qsub -v DIR=130830_SN911_0178_BD2C1VACXX ~/bin/sftp.bio-backup.pbs
2559108.crunch.local

PBS Job Id: 2559108.crunch.local
Job Name:   sftp.bio-backup
Exec host:  compute-13-13/9
Execution terminated
Exit_status=0
resources_used.cput=01:08:56
resources_used.mem=10140kb
resources_used.vmem=275728kb
resources_used.walltime=01:23:19

[smondet]

Swapped lanes 7 and 8 and

hitscore production b2f start -user sm4431 -force-new-samplesheet -bases-mask Y*,I8,I8,Y* /scratch/gencore/hiseq-700911/130830_SN911_0178_BD2C1VACXX/

Assemble_sample_sheet.run succeeded
Last inaccessible_hiseq_raw: 5740 on 2012-01-18 10:14:00.861864-05:00
Evaluation 34439 started.

PBS Job Id: 2607057.crunch.local
Job Name:   HS-B2F-34439-D2C1VACXX_2013-10-02_10-52-51.111117
Exec host:  compute-12-31/7+compute-12-31/6+compute-12-31/5+compute-12-31/4+compute-12-31/3+compute-12-31/2+compute-12-31/1+compute-12-31/0
Execution terminated
Exit_status=0
resources_used.cput=30:14:51
resources_used.mem=1044024kb
resources_used.vmem=4219376kb
resources_used.walltime=11:12:41

gencore@bowery-0-3:~ $ hitscore production fxqs start -user sm4431 -from-b2f 34439

Creating VFS link (coerce_b2f_unaligned)
Evaluation 34463 started!

PBS Job Id: 2608784.crunch.local
Job Name:   hs_fxqs_34463
Exec host:  compute-12-9/0
Execution terminated
Exit_status=0
resources_used.cput=05:09:26
resources_used.mem=33092kb
resources_used.vmem=436576kb
resources_used.walltime=05:36:47

 $ hitscore production deliver 34439 31474 $GOUT 2013-08-27-fixed
bowery2.local has address 128.122.215.15
unaligned_path: "/data/cgsb/gencore//vol/bcl_to_fastq/000034453_B2F34439_Raw31485_Sash34437/Unaligned/"
pi: Rockman; lanes: 30684, 30880, 31076, 31272, 31424, 31448, 31472
Rockman wants lanes: 1, 2, 3, 4, 5, 7, 6 of D2C1VACXX
logins: jpn3, lmn3, mr176
created links dir: /data/cgsb/gencore/out/Rockman/2013-08-27-fixed_D2C1VACXX
aa144 : cgsb users
sm4431 : cgsb users
ps103 : cgsb users carlton
id: jsd6: No such user
kw1213 : cgsb users
carltj01 : cgsb users carlton
id: jpn3: No such user
lmn3 : cgsb users
mr176 : cgsb users
Done: Preparation: 34484