27-Aug-2013 C2FEJACXX - Purugganan Rachel

[smondet]

RUNID=130830_SN911_0177_AC2FEJACXX

• [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]

 $ qsub -v DIR=130830_SN911_0177_AC2FEJACXX bin/rsync.pbs 
2520969.crunch.local

PBS Job Id: 2520969.crunch.local
Job Name:   hiseq-rsync
Exec host:  compute-12-4/0
Execution terminated
Exit_status=0
resources_used.cput=01:40:56
resources_used.mem=259676kb
resources_used.vmem=613292kb
resources_used.walltime=22:19:58

[smondet]

 $ hitscore production b2f start $PWD/130830_SN911_0177_AC2FEJACXX

FAILS WITH:

[2013-09-16 10:49:18]   [configureBclToFastq.pl]        INFO: Guessed use-bases mask: yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy,IIIIIIIn,IIIIIIIn,yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy
[2013-09-16 10:49:18]   [configureBclToFastq.pl]        ERROR: barcode GAGATTCCTATAGCCT for lane 2 has length 16: expected barcode lenth (including delimiters) is 14

[smondet]

 $ hitscore production b2f start -bases-mask 'Y*,I8,I8,Y*' $PWD/130830_SN911_0177_AC2FEJACXX

Assemble_sample_sheet.run hit a previously ran assembly
Last inaccessible_hiseq_raw: 5740 on 2012-01-18 10:14:00.861864-05:00
Evaluation 31518 started.

KILLED

[smondet]

 $ qsub -v DIR=130830_SN911_0177_AC2FEJACXX ~/bin/rsync.pbs 
2528902.crunch.local

PBS Job Id: 2528902.crunch.local
Job Name:   hiseq-rsync
Exec host:  compute-13-0/7
Execution terminated
Exit_status=0
resources_used.cput=00:44:14
resources_used.mem=259632kb
resources_used.vmem=613740kb
resources_used.walltime=25:20:05

[smondet]

Re-demux:

$ hitscore production b2f start -bases-mask 'Y*,I8,I8,Y*' $PWD/130830_SN911_0177_AC2FEJACXX -user sm4431

Assemble_sample_sheet.run hit a previously ran assembly
Last inaccessible_hiseq_raw: 5740 on 2012-01-18 10:14:00.861864-05:00
Evaluation 31700 started.

[smondet]

$ hitscore production fxqs start -user sm4431 -from-b2f 31700 
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 31789 started!

PBS Job Id: 2541524.crunch.local
Job Name:   hs_fxqs_31789
Exec host:  compute-13-24/7
Execution terminated
Exit_status=0
resources_used.cput=03:55:01
resources_used.mem=33052kb
resources_used.vmem=436376kb
resources_used.walltime=03:59:48

[smondet]

Running also:

2535473.crunch.l     gencore  cgsb-s   tar               25426     1   1 2048mb 48:00 R 18:28

PBS Job Id: 2535473.crunch.local
Job Name:   tar
Exec host:  compute-13-0/7
Execution terminated
Exit_status=0
resources_used.cput=08:32:18
resources_used.mem=5348kb
resources_used.vmem=216240kb
resources_used.walltime=35:38:04

[smondet]

 $ qsub -v DIR=130830_SN911_0177_AC2FEJACXX ~/bin/sftp.bio-backup.pbs 
2549246.crunch.local

PBS Job Id: 2549246.crunch.local
Job Name:   sftp.bio-backup
Exec host:  compute-12-5/0
Execution terminated
Exit_status=0
resources_used.cput=00:54:31
resources_used.mem=9356kb
resources_used.vmem=275028kb
resources_used.walltime=01:05:41