2013-09-10 H79WBADXX Gunsiano, Small

[agarwal]

RUNID=...

• [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=130913_SN911_0180_BH79WBADXX  bin/rsync.pbs 
2521181.crunch.local

[smondet]

PBS Job Id: 2521181.crunch.local Job Name: hiseq-rsync Exec host: compute-12-12/3 Execution terminated Exit_status=0 resources_used.cput=00:04:29 resources_used.mem=21756kb resources_used.vmem=360528kb resources_used.walltime=02:17:30

[smondet]

 $ qsub -v DIR=130913_SN911_0180_BH79WBADXX  ~/bin/tar.pbs
2527451.crunch.local

PBS Job Id: 2527451.crunch.local
Job Name:   tar
Exec host:  compute-13-23/0
Execution terminated
Exit_status=0
resources_used.cput=00:37:12
resources_used.mem=5324kb
resources_used.vmem=215988kb
resources_used.walltime=02:42:18

[smondet]

hitscore production b2f start $PWD/130913_SN911_0180_BH79WBADXX

Evaluation 31657 started.

2534150.crunch.l     gencore  cgsb-s   HS-B2F-31657-H79    --      1   8 16384m 48:00 Q   -- 

[smondet]

 $ hitscore production fxqs start -from-b2f 31657  -user sm4431
Evaluation 31680 started!

[smondet]

 $ qsub -v DIR=130913_SN911_0180_BH79WBADXX ~/bin/sftp.bio-backup.pbs 
2535330.crunch.local

PBS Job Id: 2535330.crunch.local
Job Name:   sftp.bio-backup
Exec host:  compute-12-12/8
Execution terminated
Exit_status=0
resources_used.cput=00:02:20
resources_used.mem=10000kb
resources_used.vmem=275584kb
resources_used.walltime=00:03:00

checked file size

[smondet]

Re-demux

$ hitscore production b2f start  /scratch/gencore/hiseq-700911/130913_SN911_0180_BH79WBADXX/ -force-new-samplesheet -user sm4431

Assemble_sample_sheet.run succeeded
Last inaccessible_hiseq_raw: 5740 on 2012-01-18 10:14:00.861864-05:00
Evaluation 31737 started.

[smondet]

 $ hitscore production fxqs start -user sm4431 -from-b2f 31737
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 31760 started!

[smondet]

 $ qsub -v DIR=130913_SN911_0180_BH79WBADXX  ~/bin/sftp.bio-backup.pbs 
2541528.crunch.local

PBS Job Id: 2541528.crunch.local
Job Name:   sftp.bio-backup
Exec host:  compute-13-24/8
Execution terminated
Exit_status=0
resources_used.cput=00:00:00
resources_used.mem=0kb
resources_used.vmem=0kb
resources_used.walltime=00:00:01

[smondet]

 $ hitscore production deliver 31737 31631 /data/cgsb/gencore/out 2013-09-10
bowery2.local has address 128.122.215.15
unaligned_path: "/data/cgsb/gencore//vol/bcl_to_fastq/000031750_B2F31737_Raw31650_Sash31735/Unaligned/"
pi: Small; lanes: 31629
Small wants lanes: 1 of H79WBADXX
logins: rrd5, sjs1
created links dir: /data/cgsb/gencore/out/Small/2013-09-10_H79WBADXX
aa144 : cgsb users
sm4431 : cgsb users
ps103 : cgsb users carlton
id: jsd6: No such user
kw1213 : cgsb users
carltj01 : cgsb users carlton
id: rrd5: No such user
id: sjs1: No such user
Done: Preparation: 31833