2013-09-10 H7D37ADXX RAPID Birnbaum

cgsb / hitscore

NYU CGSB Genomics Core Facility

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2013-09-10 H7D37ADXX RAPID Birnbaum #110

Closed agarwal closed 10 years ago

agarwal commented 11 years ago

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 commented 10 years ago

gencore@bowery-0-3:~ $ qsub -v DIR=130913_SN911_0179_AH7D37ADXX bin/rsync.pbs
2521180.crunch.local

smondet commented 10 years ago

PBS Job Id: 2521180.crunch.local Job Name: hiseq-rsync Exec host: compute-12-14/7 Execution terminated Exit_status=0 resources_used.cput=00:10:28 resources_used.mem=31444kb resources_used.vmem=370456kb resources_used.walltime=03:31:21

smondet commented 10 years ago

hitscore production b2f start /scratch/gencore/hiseq-700911/130913_SN911_0179_AH7D37ADXX/
2522785.crunch.l     gencore  cgsb-s   HS-B2F-27041-H7D    611     1   8 16384m 48:00 R   --

Failed because of barcode collision AAGACG Vs ATCACG (Illumina 1)

 $ hitscore production b2f start -mismatch-zero /scratch/gencore/hiseq-700911/130913_SN911_0179_AH7D37ADXX/
Evaluation 27056 started.

2522796.crunch.l     gencore  cgsb-s   HS-B2F-27056-H7D   5083     1   8 16384m 48:00 R   --

smondet commented 10 years ago

 $ qsub -v DIR=130913_SN911_0179_AH7D37ADXX  ~/bin/tar.pbs
2527446.crunch.local

PBS Job Id: 2527446.crunch.local
Job Name:   tar
Exec host:  compute-13-12/0
Execution terminated
Exit_status=0
resources_used.cput=01:01:50
resources_used.mem=5356kb
resources_used.vmem=215916kb
resources_used.walltime=03:47:58

smondet commented 10 years ago

 $ qsub -v DIR=130913_SN911_0179_AH7D37ADXX  ~/bin/sftp.bio-backup.pbs 
2529214.crunch.local

PBS Job Id: 2529214.crunch.local
Job Name:   sftp.bio-backup
Exec host:  compute-13-0/1
Execution terminated
Exit_status=0
resources_used.cput=00:06:47
resources_used.mem=9724kb
resources_used.vmem=275392kb
resources_used.walltime=00:07:16