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cgsb / hitscore

NYU CGSB Genomics Core Facility
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17 Sept 2013 (FCID: H7D3MADXX) Moin / Jasmine #115

Closed smondet closed 10 years ago

smondet commented 10 years ago
smondet commented 10 years ago 
On Pod in /hiseq
==  $    GZIP=-2 nice time tar  --exclude=Data/Intensities/L00*/C*.1  -czf \
  ~/130919_SN911_0181_AH7D3MADXX.tar.gz 130919_SN911_0181_AH7D3MADXX

7161.70user 357.63system 3:23:10elapsed 61%CPU (0avgtext+0avgdata 5392maxresident)k
270284832inputs+197365024outputs (4major+707minor)pagefaults 0swaps

==  $ echo $?
0

$ qsub -v DIR=130919_SN911_0181_AH7D3MADXX rsync-tar.pbs
2585075.crunch.local

PBS Job Id: 2585075.crunch.local
Job Name:   tar-hiseq-rsync
Exec host:  compute-12-18/9
Execution terminated
Exit_status=0
resources_used.cput=00:23:04
resources_used.mem=8684kb
resources_used.vmem=347592kb
resources_used.walltime=01:03:31
smondet commented 10 years ago 
 $ qsub -v DIR=130919_SN911_0181_AH7D3MADXX ~/bin/untar.pbs 
2585309.crunch.local

PBS Job Id: 2585309.crunch.local
Job Name:   tar
Exec host:  compute-12-1/0
Execution terminated
Exit_status=0
resources_used.cput=00:35:37
resources_used.mem=4388kb
resources_used.vmem=216060kb
resources_used.walltime=14:27:29
smondet commented 10 years ago 
 $ hitscore production b2f start -user sm4431 -bases-mask Y*,I8,I8,Y*  /scratch/gencore/hiseq-700911/130919_SN911_0181_AH7D3MADXX

Assemble_sample_sheet.run succeeded
Last inaccessible_hiseq_raw: 5740 on 2012-01-18 10:14:00.861864-05:00
Evaluation 33568 started.

PBS Job Id: 2586244.crunch.local
Job Name:   HS-B2F-33568-H7D3MADXX_2013-09-27_10-02-48.760231
Exec host:  compute-12-23/7+compute-12-23/6+compute-12-23/5+compute-12-23/4+compute-12-23/3+compute-12-23/2+compute-12-23/1+compute-12-23/0
Execution terminated
Exit_status=0
resources_used.cput=04:19:16
resources_used.mem=228028kb
resources_used.vmem=2923404kb
resources_used.walltime=01:29:35
smondet commented 10 years ago 
 $ qsub -v DIR=130919_SN911_0181_AH7D3MADXX ~/bin/sftp.bio-backup.pbs 
2586246.crunch.local

PBS Job Id: 2586246.crunch.local
Job Name:   sftp.bio-backup
Exec host:  compute-13-25/4
Execution terminated
Exit_status=0
resources_used.cput=00:20:01
resources_used.mem=9824kb
resources_used.vmem=275464kb
resources_used.walltime=00:22:28
smondet commented 10 years ago 
 $ time md5sum 130919_SN911_0181_AH7D3MADXX.tar.gz > `date +%F.%T`.130919_SN911_0181_AH7D3MADXX.tar.gz.md5

real    5m14.100s
user    3m16.482s
sys     1m37.635s

 $ cat 2013-09-27.10\:10\:13.130919_SN911_0181_AH7D3MADXX.tar.gz.md5 
2eb475a0ab655774d1284c1cd66cd2da  130919_SN911_0181_AH7D3MADXX.tar.gz

sm4431@pod:    0 jobs in ~
==  $ time nice md5sum 130919_SN911_0181_AH7D3MADXX.tar.gz
2eb475a0ab655774d1284c1cd66cd2da  130919_SN911_0181_AH7D3MADXX.tar.gz

real    14m21.763s
user    4m13.997s
sys     1m8.985s

 sm4431@pod:    0 jobs in ~
==  $ rm 130919_SN911_0181_AH7D3MADXX.tar.gz
smondet commented 10 years ago 
 $ hitscore production fxqs start -user sm4431 -from-b2f 33568

Evaluation 33591 started!

PBS Job Id: 2587658.crunch.local
Job Name:   hs_fxqs_33591
Exec host:  compute-13-2/10
Execution terminated
Exit_status=0
resources_used.cput=01:29:36
resources_used.mem=33124kb
resources_used.vmem=436316kb
resources_used.walltime=01:30:30
smondet commented 10 years ago

New demultiplxing with CASAVA:

hitscore production b2f start -user sm4431 -bases-mask Y*,Y*,Y*,Y*  -no-demux /scratch/gencore/hiseq-700911/130919_SN911_0181_AH7D3MADXX

Evaluation 33616 started.

PBS Job Id: 2597637.crunch.local
Job Name:   HS-B2F-33616-H7D3MADXX_2013-09-30_10-21-13.573603
Exec host:  compute-12-10/10+compute-12-10/9+compute-12-10/7+compute-12-10/4+compute-12-10/3+compute-12-10/2+compute-12-10/1+compute-12-10/0
Execution terminated
Exit_status=0
resources_used.cput=03:48:20
resources_used.mem=231096kb
resources_used.vmem=2838740kb
resources_used.walltime=01:11:05
smondet commented 10 years ago 
from:    Sebastien Mondet <sebastien.mondet@nyu.edu>
to:  Illumina Technical Support <techsupport@illumina.com>
cc:  Paul Scheid <ps103@nyu.edu>
date:    Mon, Sep 30, 2013 at 12:25 PM
subject:     Problem with CASAVA (dual-indexing, rapid run)
mailed-by:   gmail.com

Hi

We have a problem using CASAVA on a dual-indexed 2x150 rapid run.

Everything seemed fine on SAV but the demultiplexer did not demultiplex anything.

I ran CASAVA with the bases-mask Y,I8,I8,Y (as discussed in SFC#00561368).

I looked into the "undetermined" FASTQ files and the sequenced index is always "NNNNNNNNNNNNNNNN" There does not seem to be any error message in the output of the scripts.

In order to investigate further I ran CASAVA with the bases-mask "Y,Y,Y,Y" and without any barcode in the sample-sheet (i.e. direct conversion BCL → FASTQ). And then we see that the reads 2 and 3 are all like this one:

@HWI-ST911:181:H7D3MADXX:2:1101:8564:1991 3:N:0:
NNNNNNNN
+
########

Do you have any idea of what could have happened? What should we do to investigate further?

Thanks & Regards Sebastien

→ SFC#00565632

smondet commented 10 years ago 
$ hitscore production b2f start -user sm4431 -bases-mask Y*,I8,I8,Y* -force-new-samplesheet /scratch/gencore/hiseq-700911/130919_SN911_0181_AH7D3MADXX

Evaluation 33673 started.

PBS Job Id: 2603065.crunch.local
Job Name:   HS-B2F-33673-H7D3MADXX_2013-09-30_17-32-56.907316
Exec host:  compute-4-15/7+compute-4-15/6+compute-4-15/5+compute-4-15/4+compute-4-15/3+compute-4-15/2+compute-4-15/1+compute-4-15/0
Execution terminated
Exit_status=0
resources_used.cput=05:05:04
resources_used.mem=341476kb
resources_used.vmem=2998776kb
resources_used.walltime=02:08:29
 $ hitscore production fxqs start -from-b2f 33673

Creating VFS link (coerce_b2f_unaligned)
Evaluation 33696 started!