SAM tools

Thanks
I understand now
I guess it is not relevant to my samples then, since each alignment file is a single sample from a single lane and a single library

Sent from my iPad

On Nov 30, 2011, at 9:20 AM, Alec Wysoker <alecw@...> wrote:

> Hi Lucia,
> 
> Read groups allow you to track where each read came from.  E.g. for marking duplicates, it would be incorrect to mark as optical duplicates reads that were not from the same lane (assuming Illumina data), and it would be incorrect to mark as PCR duplicates reads that come from different libraries.  
> 
> -Alec
> 
> On 11/20/2011 1:44 PM, Lucia Peixoto wrote:
>> 
>> Hi,
>> 
>> None of my alignments have read groups, so I have been passing picard validation using "lenient", since it is the only error I get, and I get no warnings
>> I understand that having read groups is good/
>> 
>> Since I am completely new to Seq, and pardon my ignorance, why?
>> How can obtain them if my aligner does not report it?
>> 
>> I am working with Chip-Seq data so far, but RNA-Seq will arrive soon
>> 
>> Thanks
>> Lucia
>> 
>> 
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure 
>> contains a definitive record of customers, application performance, 
>> security threats, fraudulent activity, and more. Splunk takes this 
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> 
>> _______________________________________________
>> Samtools-help mailing list
>> Samtools-help@...
>> https://lists.sourceforge.net/lists/listinfo/samtools-help

On Nov 29, 2011, at 2:11 PM, Cittaro Davide wrote:

Hi all, would anybody recommend a way to get only reads that have been soft clipped in alignment at their beginning different from

awk '$6 ~ /^[0-9]*S/'


Forgot to say that I would retain paired end information...

d

?

Thanks

d
/*
Davide Cittaro, PhD

Head of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

Office: +39 02 26439140
Mail: cittaro.davide@...>
Skype: daweonline
*/










------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d_______________________________________________
Samtools-help mailing list
Samtools-help@...
https://lists.sourceforge.net/lists/listinfo/samtools-help

/*
Davide Cittaro, PhD

Head of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

Office: +39 02 26439140
Mail: cittaro.davide@...>
Skype: daweonline
*/

Hi, Samtools folks:

A few colleagues of mine use samtools in slightly different ways on the same data and got somewhat different results. I just wonder how you guys experience on this.

1.there are two ways to call SNPs in samtools when you have multiple samples:
         A. call all of the samples altogether use a single command: e.g., samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
         B. call sample individually (loop for each of the samples). Which way is better or does no matter?
I know GATK prefer to use more samples altogether to call SNPs, is it the same for samtools?

 2. There are a few options to use for filtering samtools mpileup SNP Calls, there is a -D option,
Under URL: http://samtools.sourceforge.net/mpileup.shtml, the suggested command is
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

But under http://samtools.sourceforge.net/samtools.shtml, the suggested command is:
Call SNPs and short indels for multiple diploid individuals:
samtools mpileup -P ILLUMINA -ugf ref.fa *.bam | bcftools view -bcvg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcf

some others use -D 1000
is there more objective way/tool to pre-assess  what value optimal for -D option (e.g., 100, 2000 or others)?

 3 also for filtering samtools mpileup SNP calls, -d option was also used. Some used -d 10 arbitrarily whereas the default is 2. Any suggestion on this aspect?

Thanks in advance for your comments or suggestions.

Best

Ming




Ming Yi, Ph.D.
Functional Genomics
Information System Program
SAIC-Frederick, Inc.
National Cancer Institute at Frederick
Post Office Box B,
Frederick, MD 21702
Phone: 301-846-5764
Fax: 301-846-7070
myi@...>
________________________________

Hi, Dear Wes:



Thanks so much for your great input, which is very helpful! Really appreciated!





Could you please see my follow-up comments and questions in red right after yours as below? Hope you have any input for those as well.



Thanks again!



Ming







-----Original Message-----
From: Barris, Wes [mailto:Wes.Barris@...]
Sent: Wednesday, November 30, 2011 2:00 PM
To: Yi, Ming (NIH/NCI) [C]; Samtools-help help
Subject: RE: Questions on samtools usage.



Yi, Ming (NIH/NCI) [C] wrote on 2011-11-29:



> Hi, Samtools folks:

>

> A few colleagues of mine use samtools in slightly different ways on

> the same data and got somewhat different results. I just wonder how

> you guys experience on this.



These are all good questions.  Let me take a stab at this...



> 1.there are two ways to call SNPs in samtools when you have multiple

> samples:

>

>          A. call all of the samples altogether use a single command:

> e.g., samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -

> bvcg - > var.raw.bcf

>

>          B. call sample individually (loop for each of the samples).

> Which way is better or does no matter?



I've done both methods that you describe.  I've recently worked with

two pools of samples where I wanted to find SNPs that differentiate

the two pools.  I supplied both sample1.bam and sample2.bam to the

mpileup command and then bcftools pair calling.  SNPs are called using

the combination of the two pools and the resulting vcf file will show

genotypes for each sample and a "CLR" value that represents the

likelihood that the genotypes are different between the samples.

I find this very useful.



What you saying seems indicating that calling samples together is better like GATK does, right? However, we did see somewhat significant difference in calling when calling samples altogether or individually, although waiting to be validated. What do you think?



> I know GATK prefer to use more samples altogether to call SNPs, is it

> the same for samtools?

>

>

>

>  2. There are a few options to use for filtering samtools mpileup SNP

> Calls, there is a -D option,

>

> Under URL: http://samtools.sourceforge.net/mpileup.shtml, the

> suggested command is

>

> samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg -

> > var.raw.bcf

>

> bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

>

>

>

> But under http://samtools.sourceforge.net/samtools.shtml, the

> suggested command is:

>

> Call SNPs and short indels for multiple diploid individuals:

>

> samtools mpileup -P ILLUMINA -ugf ref.fa *.bam | bcftools view -bcvg -

>> var.raw.bcf

>

> bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 >

> var.flt.vcf

>

>

>

> some others use -D 1000

>

> is there more objective way/tool to pre-assess  what value optimal for

> -D option (e.g., 100, 2000 or others)?



The -D option is used to specify maximum read depth.  The value you use

will depend on your expected coverage.  For example, if you are analyzing

two samples each with 30x coverage, you would expect 60x coverage.  If you

want to prevent from calling SNPs in potential CNV areas, you might want

to limit SNP calling to a maximum read depth of 2 times the expected coverage

or 120 (-D 120).  At least that is how I interpret it.



Great suggestions!! What about -d? have you tried on it or just use default (or -d at 2)?



>  3 also for filtering samtools mpileup SNP calls, -d option was also

> used. Some used -d 10 arbitrarily whereas the default is 2. Any

> suggestion on this aspect?

>

>

>

> Thanks in advance for your comments or suggestions.

>

>

>

> Best

>

>

>

> Ming

>

>

>

>

>

>

>

>

>

> Ming Yi, Ph.D.

> Functional Genomics

> Information System Program

> SAIC-Frederick, Inc.

> National Cancer Institute at Frederick Post Office Box B, Frederick,

> MD 21702

> Phone: 301-846-5764

> Fax: 301-846-7070

> myi@...

>

> ________________________________

>

>





--

Wes Barris





This email and any files transmitted with it are confidential and intended solely for the use of the addressee. If you are not the intended addressee, then you have received this email in error and any use, dissemination, forwarding, printing, or copying of this email is strictly prohibited. Please notify us immediately of your unintended receipt by reply and then delete this email and your reply. Cobb-Vantress, Inc. and its subsidiaries and affiliates will not be held liable to any person resulting from the unintended or unauthorized use of any information contained in this email or as a result of any additions or deletions of information originally contained in this email.

On Wed, Nov 30, 2011 at 2:21 PM, Yi, Ming (NIH/NCI) [C] <yiming@...
> wrote:

> ** ** **
>
> Hi, Dear Wes:****
>
> ** **
>
> Thanks so much for your great input, which is very helpful! Really
> appreciated!****
>
> ** **
>
> ** **
>
> Could you please see my follow-up comments and questions in red right
> after yours as below? Hope you have any input for those as well. ****
>
> ** **
>
> Thanks again!****
>
> ** **
>
> Ming****
>
> ** **
>
> ** **
>
> ** **
>
> -----Original Message-----
> From: Barris, Wes [mailto:Wes.Barris@...]
> Sent: Wednesday, November 30, 2011 2:00 PM
> To: Yi, Ming (NIH/NCI) [C]; Samtools-help help
> Subject: RE: Questions on samtools usage.
>
> ** **
>
> Yi, Ming (NIH/NCI) [C] wrote on 2011-11-29:****
>
> ** **
>
> > Hi, Samtools folks:****
>
> > ****
>
> > A few colleagues of mine use samtools in slightly different ways on ****
>
> > the same data and got somewhat different results. I just wonder how ****
>
> > you guys experience on this.****
>
> ** **
>
> These are all good questions.  Let me take a stab at this...****
>
> ** **
>
> > 1.there are two ways to call SNPs in samtools when you have multiple****
>
> > samples:****
>
> > ****
>
> >          A. call all of the samples altogether use a single command:****
>
> > e.g., samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view - **
> **
>
> > bvcg - > var.raw.bcf****
>
> > ****
>
> >          B. call sample individually (loop for each of the samples).****
>
> > Which way is better or does no matter?****
>
> ** **
>
> I've done both methods that you describe.  I've recently worked with****
>
> two pools of samples where I wanted to find SNPs that differentiate****
>
> the two pools.  I supplied both sample1.bam and sample2.bam to the****
>
> mpileup command and then bcftools pair calling.  SNPs are called using****
>
> the combination of the two pools and the resulting vcf file will show****
>
> genotypes for each sample and a "CLR" value that represents the****
>
> likelihood that the genotypes are different between the samples.****
>
> I find this very useful.****
>
> ** **
>
> What you saying seems indicating that calling samples together is better
> like GATK does, right? However, we did see somewhat significant difference
> in calling when calling samples altogether or individually, although
> waiting to be validated. What do you think?****
>
> **
>

Hi, Ming.  Generally, you are not going to lose much by calling together
and have a lot to gain (in terms of sensitivity).  If you have many
samples, I think there is a bias against finding a rare variant, but for
two samples, I don't think you will see that bias.  Perhaps Heng has more
enlightened comments on the subject, though.


> **
>
> > I know GATK prefer to use more samples altogether to call SNPs, is it **
> **
>
> > the same for samtools?****
>
> > ****
>
> > ****
>
> > ****
>
> >  2. There are a few options to use for filtering samtools mpileup SNP **
> **
>
> > Calls, there is a -D option,****
>
> > ****
>
> > Under URL: http://samtools.sourceforge.net/mpileup.shtml, the ****
>
> > suggested command is****
>
> > ****
>
> > samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - **
> **
>
> > > var.raw.bcf****
>
> > ****
>
> > bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf***
> *
>
> > ****
>
> > ****
>
> > ****
>
> > But under http://samtools.sourceforge.net/samtools.shtml, the ****
>
> > suggested command is:****
>
> > ****
>
> > Call SNPs and short indels for multiple diploid individuals:****
>
> > ****
>
> > samtools mpileup -P ILLUMINA -ugf ref.fa *.bam | bcftools view -bcvg -**
> **
>
> >> var.raw.bcf****
>
> > ****
>
> > bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > ****
>
> > var.flt.vcf****
>
> > ****
>
> > ****
>
> > ****
>
> > some others use -D 1000****
>
> > ****
>
> > is there more objective way/tool to pre-assess  what value optimal for *
> ***
>
> > -D option (e.g., 100, 2000 or others)?****
>
> ** **
>
> The -D option is used to specify maximum read depth.  The value you use***
> *
>
> will depend on your expected coverage.  For example, if you are analyzing*
> ***
>
> two samples each with 30x coverage, you would expect 60x coverage.  If you
> ****
>
> want to prevent from calling SNPs in potential CNV areas, you might want**
> **
>
> to limit SNP calling to a maximum read depth of 2 times the expected
> coverage****
>
> or 120 (-D 120).  At least that is how I interpret it.****
>
> ** **
>
> Great suggestions!! What about –d? have you tried on it or just use
> default (or –d at 2)?****
>
> **
>

Depth filtering is only the roughest of filters and there is not an
absolute cutoff.  I'd suggest using a low threshold (2, for example) and
then filtering based on depth, QD, strand bias, etc.  See the GATK variant
evaluation and recalibration tools for some ideas about filtering criteria.


Sean


> **
>
> >  3 also for filtering samtools mpileup SNP calls, -d option was also ***
> *
>
> > used. Some used -d 10 arbitrarily whereas the default is 2. Any ****
>
> > suggestion on this aspect?****
>
> > ****
>
> > ****
>
> > ****
>
> > Thanks in advance for your comments or suggestions.****
>
> > ****
>
> > ****
>
> > ****
>
> > Best****
>
> > ****
>
> > ****
>
> > ****
>
> > Ming****
>
> > ****
>
> > ****
>
> > ****
>
> > ****
>
> > ****
>
> > ****
>
> > ****
>
> > ****
>
> > ****
>
> > **Ming Yi**, Ph.D.****
>
> > Functional Genomics****
>
> > Information System Program****
>
> > SAIC-Frederick, Inc.****
>
> > National Cancer Institute at **Frederick** Post Office Box B, ****
> Frederick****, ****
>
> > MD 21702****
>
> > Phone: 301-846-5764****
>
> > Fax: 301-846-7070****
>
> > myi@...****
>
> > ****
>
> > ________________________________****
>
> > ****
>
> >** **
>
> ** **
>
> ** **
>
> --****
>
> Wes Barris****
>
> ** **
>
> ** **
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the addressee. If you are not the intended addressee,
> then you have received this email in error and any use, dissemination,
> forwarding, printing, or copying of this email is strictly prohibited.
> Please notify us immediately of your unintended receipt by reply and then
> delete this email and your reply. Cobb-Vantress, Inc. and its subsidiaries
> and affiliates will not be held liable to any person resulting from the
> unintended or unauthorized use of any information contained in this email
> or as a result of any additions or deletions of information originally
> contained in this email.****
>

Yi, Ming (NIH/NCI) [C] wrote on 2011-11-30:

> I've done both methods that you describe.  I've recently worked with
> two pools of samples where I wanted to find SNPs that differentiate
> the two pools.  I supplied both sample1.bam and sample2.bam to the
> mpileup command and then bcftools pair calling.  SNPs are called using
> the combination of the two pools and the resulting vcf file will show
> genotypes for each sample and a "CLR" value that represents the
> likelihood that the genotypes are different between the samples.
> I find this very useful.
> 
> What you saying seems indicating that calling samples together is
> better like GATK does, right? However, we did see somewhat significant
> difference in calling when calling samples altogether or individually,
> although waiting to be validated. What do you think?

It is very difficult to call SNPs independently in two (pooled) samples
and then try to find differences.  It depends on exactly what you are
trying to find.

> The -D option is used to specify maximum read depth.  The value you use
> will depend on your expected coverage.  For example, if you are analyzing
> two samples each with 30x coverage, you would expect 60x coverage.  If
> you
> want to prevent from calling SNPs in potential CNV areas, you might want
> to limit SNP calling to a maximum read depth of 2 times the expected
> coverage
> or 120 (-D 120).  At least that is how I interpret it.
> 
> Great suggestions!! What about -d? have you tried on it or just use
> default (or -d at 2)?

I have not used -d.

>>  3 also for filtering samtools mpileup SNP calls, -d option was also
> 
>> used. Some used -d 10 arbitrarily whereas the default is 2. Any
>> 
>> suggestion on this aspect?
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Thanks in advance for your comments or suggestions.
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Best
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Ming
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Ming Yi, Ph.D.
>> 
>> Functional Genomics
>> 
>> Information System Program
>> 
>> SAIC-Frederick, Inc.
>> 
>> National Cancer Institute at Frederick Post Office Box B, Frederick,
>> 
>> MD 21702
>> 
>> Phone: 301-846-5764
>> 
>> Fax: 301-846-7070
>> 
>> myi@...
>> 
>> 
>> 
>> ________________________________
>> 
>> 
>> 
>> 
> 
> 
> 
> 
>


--
Wes Barris


This email and any files transmitted with it are confidential and intended solely for the use of the addressee. If you are not the intended addressee, then you have received this email in error and any use, dissemination, forwarding, printing, or copying of this email is strictly prohibited. Please notify us immediately of your unintended receipt by reply and then delete this email and your reply. Cobb-Vantress, Inc. and its subsidiaries and affiliates will not be held liable to any person resulting from the unintended or unauthorized use of any information contained in this email or as a result of any additions or deletions of information originally contained in this email.

Yi, Ming (NIH/NCI) [C] wrote on 2011-11-29:

> Hi, Samtools folks:
> 
> A few colleagues of mine use samtools in slightly different ways on 
> the same data and got somewhat different results. I just wonder how 
> you guys experience on this.

These are all good questions.  Let me take a stab at this...

> 1.there are two ways to call SNPs in samtools when you have multiple
> samples:
> 
>          A. call all of the samples altogether use a single command:
> e.g., samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view - 
> bvcg - > var.raw.bcf
> 
>          B. call sample individually (loop for each of the samples).
> Which way is better or does no matter?

I've done both methods that you describe.  I've recently worked with
two pools of samples where I wanted to find SNPs that differentiate
the two pools.  I supplied both sample1.bam and sample2.bam to the
mpileup command and then bcftools pair calling.  SNPs are called using
the combination of the two pools and the resulting vcf file will show
genotypes for each sample and a "CLR" value that represents the
likelihood that the genotypes are different between the samples.
I find this very useful.

> I know GATK prefer to use more samples altogether to call SNPs, is it 
> the same for samtools?
> 
> 
> 
>  2. There are a few options to use for filtering samtools mpileup SNP 
> Calls, there is a -D option,
> 
> Under URL: http://samtools.sourceforge.net/mpileup.shtml, the 
> suggested command is
> 
> samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - 
> > var.raw.bcf
> 
> bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
> 
> 
> 
> But under http://samtools.sourceforge.net/samtools.shtml, the 
> suggested command is:
> 
> Call SNPs and short indels for multiple diploid individuals:
> 
> samtools mpileup -P ILLUMINA -ugf ref.fa *.bam | bcftools view -bcvg -
>> var.raw.bcf
> 
> bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > 
> var.flt.vcf
> 
> 
> 
> some others use -D 1000
> 
> is there more objective way/tool to pre-assess  what value optimal for 
> -D option (e.g., 100, 2000 or others)?

The -D option is used to specify maximum read depth.  The value you use
will depend on your expected coverage.  For example, if you are analyzing
two samples each with 30x coverage, you would expect 60x coverage.  If you
want to prevent from calling SNPs in potential CNV areas, you might want
to limit SNP calling to a maximum read depth of 2 times the expected coverage
or 120 (-D 120).  At least that is how I interpret it.


>  3 also for filtering samtools mpileup SNP calls, -d option was also 
> used. Some used -d 10 arbitrarily whereas the default is 2. Any 
> suggestion on this aspect?
> 
> 
> 
> Thanks in advance for your comments or suggestions.
> 
> 
> 
> Best
> 
> 
> 
> Ming
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Ming Yi, Ph.D.
> Functional Genomics
> Information System Program
> SAIC-Frederick, Inc.
> National Cancer Institute at Frederick Post Office Box B, Frederick, 
> MD 21702
> Phone: 301-846-5764
> Fax: 301-846-7070
> myi@...
> 
> ________________________________
> 
>


--
Wes Barris


This email and any files transmitted with it are confidential and intended solely for the use of the addressee. If you are not the intended addressee, then you have received this email in error and any use, dissemination, forwarding, printing, or copying of this email is strictly prohibited. Please notify us immediately of your unintended receipt by reply and then delete this email and your reply. Cobb-Vantress, Inc. and its subsidiaries and affiliates will not be held liable to any person resulting from the unintended or unauthorized use of any information contained in this email or as a result of any additions or deletions of information originally contained in this email.

Hi Ellul,

I recently discovered a bug in MergeSamFiles with USE_THREADING=true.  
This bug has been fixed in the source code repository, but we have had a 
delay in pushing out a new build.  If you can check out and build the 
trunk source code, the hang should no longer happen.  If you can't do 
that, don't USE_THREADING=true.  I hope to push out a new build on 
Monday, but I can't promise that.

-Alec


On 11/25/2011 9:30 AM, Ellul Jason wrote:
> Hi all,
>
> Sometimes when I am running MergeSamFiles picard hangs and stops processing the bam files. Here is a thread dump from an example of when it hung:
>
> 2011-11-26 01:22:25
> Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.2-b06 mixed mode):
>
> "Thread-0" prio=10 tid=0x00007f93d818f800 nid=0x1e3f waiting on condition [0x00007f93c5d2f000]
>     java.lang.Thread.State: WAITING (parking)
> 	at sun.misc.Unsafe.park(Native Method)
> 	- parking to wait for<0x0000000700006768>  (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
> 	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:156)
> 	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
> 	at java.util.concurrent.ArrayBlockingQueue.put(ArrayBlockingQueue.java:252)
> 	at net.sf.picard.sam.MergeSamFiles$1.run(MergeSamFiles.java:155)
> 	at java.lang.Thread.run(Thread.java:662)
>
> "Low Memory Detector" daemon prio=10 tid=0x00007f93d80c9000 nid=0x1e39 runnable [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "C2 CompilerThread1" daemon prio=10 tid=0x00007f93d80c7000 nid=0x1e38 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "C2 CompilerThread0" daemon prio=10 tid=0x00007f93d80c4000 nid=0x1e37 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "Signal Dispatcher" daemon prio=10 tid=0x00007f93d80c2000 nid=0x1e36 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "Finalizer" daemon prio=10 tid=0x00007f93d80a5800 nid=0x1e35 in Object.wait() [0x00007f93c644c000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
> 	- locked<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
> 	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
>
> "Reference Handler" daemon prio=10 tid=0x00007f93d80a3800 nid=0x1e34 in Object.wait() [0x00007f93c654d000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
> 	at java.lang.Object.wait(Object.java:485)
> 	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
> 	- locked<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>
> "main" prio=10 tid=0x00007f93d8006800 nid=0x1e25 in Object.wait() [0x00007f93dcc9f000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x0000000700024c20>  (a java.lang.Thread)
> 	at java.lang.Thread.join(Thread.java:1186)
> 	- locked<0x0000000700024c20>  (a java.lang.Thread)
> 	at java.lang.Thread.join(Thread.java:1239)
> 	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:190)
> 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
> 	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:84)
>
> "VM Thread" prio=10 tid=0x00007f93d809d000 nid=0x1e33 runnable
>
> "GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f93d8019800 nid=0x1e26 runnable
>
> "GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f93d801b800 nid=0x1e27 runnable
>
> "GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f93d801d800 nid=0x1e28 runnable
>
> "GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f93d801f000 nid=0x1e29 runnable
>
> "GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f93d8021000 nid=0x1e2a runnable
>
> "GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f93d8023000 nid=0x1e2b runnable
>
> "GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f93d8024800 nid=0x1e2c runnable
>
> "GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f93d8026800 nid=0x1e2d runnable
>
> "GC task thread#8 (ParallelGC)" prio=10 tid=0x00007f93d8028000 nid=0x1e2e runnable
>
> "GC task thread#9 (ParallelGC)" prio=10 tid=0x00007f93d802a000 nid=0x1e2f runnable
>
> "GC task thread#10 (ParallelGC)" prio=10 tid=0x00007f93d802c000 nid=0x1e30 runnable
>
> "GC task thread#11 (ParallelGC)" prio=10 tid=0x00007f93d802d800 nid=0x1e31 runnable
>
> "GC task thread#12 (ParallelGC)" prio=10 tid=0x00007f93d802f800 nid=0x1e32 runnable
>
> "VM Periodic Task Thread" prio=10 tid=0x00007f93d80dc000 nid=0x1e3a waiting on condition
>
> JNI global references: 1074
>
> Heap
>   PSYoungGen      total 932096K, used 17959K [0x00000007aaab0000, 0x0000000800000000, 0x0000000800000000)
>    eden space 466112K, 3% used [0x00000007aaab0000,0x00000007abc39d90,0x00000007c71e0000)
>    from space 465984K, 0% used [0x00000007e38f0000,0x00000007e38f0000,0x0000000800000000)
>    to   space 465984K, 0% used [0x00000007c71e0000,0x00000007c71e0000,0x00000007e38f0000)
>   PSOldGen        total 1399808K, used 704584K [0x0000000700000000, 0x0000000755700000, 0x00000007aaab0000)
>    object space 1399808K, 50% used [0x0000000700000000,0x000000072b012048,0x0000000755700000)
>   PSPermGen       total 21248K, used 6322K [0x00000006fae00000, 0x00000006fc2c0000, 0x0000000700000000)
>    object space 21248K, 29% used [0x00000006fae00000,0x00000006fb42c998,0x00000006fc2c0000)
>
> 2011-11-26 01:22:33
> Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.2-b06 mixed mode):
>
> "Thread-0" prio=10 tid=0x00007f93d818f800 nid=0x1e3f waiting on condition [0x00007f93c5d2f000]
>     java.lang.Thread.State: WAITING (parking)
> 	at sun.misc.Unsafe.park(Native Method)
> 	- parking to wait for<0x0000000700006768>  (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
> 	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:156)
> 	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
> 	at java.util.concurrent.ArrayBlockingQueue.put(ArrayBlockingQueue.java:252)
> 	at net.sf.picard.sam.MergeSamFiles$1.run(MergeSamFiles.java:155)
> 	at java.lang.Thread.run(Thread.java:662)
>
> "Low Memory Detector" daemon prio=10 tid=0x00007f93d80c9000 nid=0x1e39 runnable [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "C2 CompilerThread1" daemon prio=10 tid=0x00007f93d80c7000 nid=0x1e38 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "C2 CompilerThread0" daemon prio=10 tid=0x00007f93d80c4000 nid=0x1e37 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "Signal Dispatcher" daemon prio=10 tid=0x00007f93d80c2000 nid=0x1e36 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "Finalizer" daemon prio=10 tid=0x00007f93d80a5800 nid=0x1e35 in Object.wait() [0x00007f93c644c000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
> 	- locked<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
> 	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
>
> "Reference Handler" daemon prio=10 tid=0x00007f93d80a3800 nid=0x1e34 in Object.wait() [0x00007f93c654d000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
> 	at java.lang.Object.wait(Object.java:485)
> 	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
> 	- locked<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>
> "main" prio=10 tid=0x00007f93d8006800 nid=0x1e25 in Object.wait() [0x00007f93dcc9f000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x0000000700024c20>  (a java.lang.Thread)
> 	at java.lang.Thread.join(Thread.java:1186)
> 	- locked<0x0000000700024c20>  (a java.lang.Thread)
> 	at java.lang.Thread.join(Thread.java:1239)
> 	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:190)
> 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
> 	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:84)
>
> "VM Thread" prio=10 tid=0x00007f93d809d000 nid=0x1e33 runnable
>
> "GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f93d8019800 nid=0x1e26 runnable
>
> "GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f93d801b800 nid=0x1e27 runnable
>
> "GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f93d801d800 nid=0x1e28 runnable
>
> "GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f93d801f000 nid=0x1e29 runnable
>
> "GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f93d8021000 nid=0x1e2a runnable
>
> "GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f93d8023000 nid=0x1e2b runnable
>
> "GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f93d8024800 nid=0x1e2c runnable
>
> "GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f93d8026800 nid=0x1e2d runnable
>
> "GC task thread#8 (ParallelGC)" prio=10 tid=0x00007f93d8028000 nid=0x1e2e runnable
>
> "GC task thread#9 (ParallelGC)" prio=10 tid=0x00007f93d802a000 nid=0x1e2f runnable
>
> "GC task thread#10 (ParallelGC)" prio=10 tid=0x00007f93d802c000 nid=0x1e30 runnable
>
> "GC task thread#11 (ParallelGC)" prio=10 tid=0x00007f93d802d800 nid=0x1e31 runnable
>
> "GC task thread#12 (ParallelGC)" prio=10 tid=0x00007f93d802f800 nid=0x1e32 runnable
>
> "VM Periodic Task Thread" prio=10 tid=0x00007f93d80dc000 nid=0x1e3a waiting on condition
>
> JNI global references: 1074
>
> Heap
>   PSYoungGen      total 932096K, used 17959K [0x00000007aaab0000, 0x0000000800000000, 0x0000000800000000)
>    eden space 466112K, 3% used [0x00000007aaab0000,0x00000007abc39d90,0x00000007c71e0000)
>    from space 465984K, 0% used [0x00000007e38f0000,0x00000007e38f0000,0x0000000800000000)
>    to   space 465984K, 0% used [0x00000007c71e0000,0x00000007c71e0000,0x00000007e38f0000)
>   PSOldGen        total 1399808K, used 704584K [0x0000000700000000, 0x0000000755700000, 0x00000007aaab0000)
>    object space 1399808K, 50% used [0x0000000700000000,0x000000072b012048,0x0000000755700000)
>   PSPermGen       total 21248K, used 6322K [0x00000006fae00000, 0x00000006fc2c0000, 0x0000000700000000)
>    object space 21248K, 29% used [0x00000006fae00000,0x00000006fb42c998,0x00000006fc2c0000)
>
> 2011-11-26 01:22:43
> Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.2-b06 mixed mode):
>
> "Thread-0" prio=10 tid=0x00007f93d818f800 nid=0x1e3f waiting on condition [0x00007f93c5d2f000]
>     java.lang.Thread.State: WAITING (parking)
> 	at sun.misc.Unsafe.park(Native Method)
> 	- parking to wait for<0x0000000700006768>  (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
> 	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:156)
> 	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
> 	at java.util.concurrent.ArrayBlockingQueue.put(ArrayBlockingQueue.java:252)
> 	at net.sf.picard.sam.MergeSamFiles$1.run(MergeSamFiles.java:155)
> 	at java.lang.Thread.run(Thread.java:662)
>
> "Low Memory Detector" daemon prio=10 tid=0x00007f93d80c9000 nid=0x1e39 runnable [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "C2 CompilerThread1" daemon prio=10 tid=0x00007f93d80c7000 nid=0x1e38 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "C2 CompilerThread0" daemon prio=10 tid=0x00007f93d80c4000 nid=0x1e37 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "Signal Dispatcher" daemon prio=10 tid=0x00007f93d80c2000 nid=0x1e36 waiting on condition [0x0000000000000000]
>     java.lang.Thread.State: RUNNABLE
>
> "Finalizer" daemon prio=10 tid=0x00007f93d80a5800 nid=0x1e35 in Object.wait() [0x00007f93c644c000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
> 	- locked<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
> 	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
>
> "Reference Handler" daemon prio=10 tid=0x00007f93d80a3800 nid=0x1e34 in Object.wait() [0x00007f93c654d000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
> 	at java.lang.Object.wait(Object.java:485)
> 	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
> 	- locked<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>
> "main" prio=10 tid=0x00007f93d8006800 nid=0x1e25 in Object.wait() [0x00007f93dcc9f000]
>     java.lang.Thread.State: WAITING (on object monitor)
> 	at java.lang.Object.wait(Native Method)
> 	- waiting on<0x0000000700024c20>  (a java.lang.Thread)
> 	at java.lang.Thread.join(Thread.java:1186)
> 	- locked<0x0000000700024c20>  (a java.lang.Thread)
> 	at java.lang.Thread.join(Thread.java:1239)
> 	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:190)
> 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
> 	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:84)
>
> "VM Thread" prio=10 tid=0x00007f93d809d000 nid=0x1e33 runnable
>
> "GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f93d8019800 nid=0x1e26 runnable
>
> "GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f93d801b800 nid=0x1e27 runnable
>
> "GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f93d801d800 nid=0x1e28 runnable
>
> "GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f93d801f000 nid=0x1e29 runnable
>
> "GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f93d8021000 nid=0x1e2a runnable
>
> "GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f93d8023000 nid=0x1e2b runnable
>
> "GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f93d8024800 nid=0x1e2c runnable
>
> "GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f93d8026800 nid=0x1e2d runnable
>
> "GC task thread#8 (ParallelGC)" prio=10 tid=0x00007f93d8028000 nid=0x1e2e runnable
>
> "GC task thread#9 (ParallelGC)" prio=10 tid=0x00007f93d802a000 nid=0x1e2f runnable
>
> "GC task thread#10 (ParallelGC)" prio=10 tid=0x00007f93d802c000 nid=0x1e30 runnable
>
> "GC task thread#11 (ParallelGC)" prio=10 tid=0x00007f93d802d800 nid=0x1e31 runnable
>
> "GC task thread#12 (ParallelGC)" prio=10 tid=0x00007f93d802f800 nid=0x1e32 runnable
>
> "VM Periodic Task Thread" prio=10 tid=0x00007f93d80dc000 nid=0x1e3a waiting on condition
>
> JNI global references: 1074
>
> Heap
>   PSYoungGen      total 932096K, used 17959K [0x00000007aaab0000, 0x0000000800000000, 0x0000000800000000)
>    eden space 466112K, 3% used [0x00000007aaab0000,0x00000007abc39d90,0x00000007c71e0000)
>    from space 465984K, 0% used [0x00000007e38f0000,0x00000007e38f0000,0x0000000800000000)
>    to   space 465984K, 0% used [0x00000007c71e0000,0x00000007c71e0000,0x00000007e38f0000)
>   PSOldGen        total 1399808K, used 704584K [0x0000000700000000, 0x0000000755700000, 0x00000007aaab0000)
>    object space 1399808K, 50% used [0x0000000700000000,0x000000072b012048,0x0000000755700000)
>   PSPermGen       total 21248K, used 6322K [0x00000006fae00000, 0x00000006fc2c0000, 0x0000000700000000)
>    object space 21248K, 29% used [0x00000006fae00000,0x00000006fb42c998,0x00000006fc2c0000)
>
> Has this behavior been seen by others? Any help would be greatly appreciated.
>
> Here is how I am running it (in this case I am only inputting 1 file so it should just sort the bam file):
>
> java -Xmx4g -Djava.io.tmpdir=/data/tmp -jar /usr/local/picard/Current_jars/MergeSamFiles.jar TMP_DIR=/storage/tmp/QGwNHb6nck MAX_RECORDS_IN_RAM=1000000 I=/storage/tmp/QGwNHb6nck/778Input_TGAT_L008.bam O=/data/pipeline_in/Runs/111027_SN1055_0074_BD0F9GACXX/ProjectFolders/Project_Dale-Garsed/Sample_778Input/Alignment_778Input/778Input_aligned.bam VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true>>  /data/pipeline_in/Runs/111027_SN1055_0074_BD0F9GACXX/ProjectFolders/Project_Dale-Garsed/Sample_778Input/Alignment_778Input/Aligner.log 2>&1
>
> thanks,
>
> Jason
>
>
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Hi Alec,

Thank you for the info, I am in no rush as we are between runs. Will download the next release when it becomes available.

Thanks again,

Jason
-- 

Jason Ellul 
Bioinformatics Core Facility Systems Administrator 
Cancer Research Division

Peter MacCallum Cancer Centre 
TEL: +61 3 9656 1512 
FAX: +61 3 9656 1411 
EMAIL: jason.ellul@...  

Address: St Andrew's Place East Melbourne Victoria 3002 Australia 
Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia

On 01/12/2011, at 3:26 AM, Alec Wysoker wrote:

> Hi Ellul,
> 
> I recently discovered a bug in MergeSamFiles with USE_THREADING=true.  This bug has been fixed in the source code repository, but we have had a delay in pushing out a new build.  If you can check out and build the trunk source code, the hang should no longer happen.  If you can't do that, don't USE_THREADING=true.  I hope to push out a new build on Monday, but I can't promise that.
> 
> -Alec
> 
> 
> On 11/25/2011 9:30 AM, Ellul Jason wrote:
>> Hi all,
>> 
>> Sometimes when I am running MergeSamFiles picard hangs and stops processing the bam files. Here is a thread dump from an example of when it hung:
>> 
>> 2011-11-26 01:22:25
>> Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.2-b06 mixed mode):
>> 
>> "Thread-0" prio=10 tid=0x00007f93d818f800 nid=0x1e3f waiting on condition [0x00007f93c5d2f000]
>>    java.lang.Thread.State: WAITING (parking)
>> 	at sun.misc.Unsafe.park(Native Method)
>> 	- parking to wait for<0x0000000700006768>  (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
>> 	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:156)
>> 	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
>> 	at java.util.concurrent.ArrayBlockingQueue.put(ArrayBlockingQueue.java:252)
>> 	at net.sf.picard.sam.MergeSamFiles$1.run(MergeSamFiles.java:155)
>> 	at java.lang.Thread.run(Thread.java:662)
>> 
>> "Low Memory Detector" daemon prio=10 tid=0x00007f93d80c9000 nid=0x1e39 runnable [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "C2 CompilerThread1" daemon prio=10 tid=0x00007f93d80c7000 nid=0x1e38 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "C2 CompilerThread0" daemon prio=10 tid=0x00007f93d80c4000 nid=0x1e37 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "Signal Dispatcher" daemon prio=10 tid=0x00007f93d80c2000 nid=0x1e36 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "Finalizer" daemon prio=10 tid=0x00007f93d80a5800 nid=0x1e35 in Object.wait() [0x00007f93c644c000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
>> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
>> 	- locked<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
>> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
>> 	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
>> 
>> "Reference Handler" daemon prio=10 tid=0x00007f93d80a3800 nid=0x1e34 in Object.wait() [0x00007f93c654d000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>> 	at java.lang.Object.wait(Object.java:485)
>> 	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
>> 	- locked<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>> 
>> "main" prio=10 tid=0x00007f93d8006800 nid=0x1e25 in Object.wait() [0x00007f93dcc9f000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x0000000700024c20>  (a java.lang.Thread)
>> 	at java.lang.Thread.join(Thread.java:1186)
>> 	- locked<0x0000000700024c20>  (a java.lang.Thread)
>> 	at java.lang.Thread.join(Thread.java:1239)
>> 	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:190)
>> 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
>> 	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:84)
>> 
>> "VM Thread" prio=10 tid=0x00007f93d809d000 nid=0x1e33 runnable
>> 
>> "GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f93d8019800 nid=0x1e26 runnable
>> 
>> "GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f93d801b800 nid=0x1e27 runnable
>> 
>> "GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f93d801d800 nid=0x1e28 runnable
>> 
>> "GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f93d801f000 nid=0x1e29 runnable
>> 
>> "GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f93d8021000 nid=0x1e2a runnable
>> 
>> "GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f93d8023000 nid=0x1e2b runnable
>> 
>> "GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f93d8024800 nid=0x1e2c runnable
>> 
>> "GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f93d8026800 nid=0x1e2d runnable
>> 
>> "GC task thread#8 (ParallelGC)" prio=10 tid=0x00007f93d8028000 nid=0x1e2e runnable
>> 
>> "GC task thread#9 (ParallelGC)" prio=10 tid=0x00007f93d802a000 nid=0x1e2f runnable
>> 
>> "GC task thread#10 (ParallelGC)" prio=10 tid=0x00007f93d802c000 nid=0x1e30 runnable
>> 
>> "GC task thread#11 (ParallelGC)" prio=10 tid=0x00007f93d802d800 nid=0x1e31 runnable
>> 
>> "GC task thread#12 (ParallelGC)" prio=10 tid=0x00007f93d802f800 nid=0x1e32 runnable
>> 
>> "VM Periodic Task Thread" prio=10 tid=0x00007f93d80dc000 nid=0x1e3a waiting on condition
>> 
>> JNI global references: 1074
>> 
>> Heap
>>  PSYoungGen      total 932096K, used 17959K [0x00000007aaab0000, 0x0000000800000000, 0x0000000800000000)
>>   eden space 466112K, 3% used [0x00000007aaab0000,0x00000007abc39d90,0x00000007c71e0000)
>>   from space 465984K, 0% used [0x00000007e38f0000,0x00000007e38f0000,0x0000000800000000)
>>   to   space 465984K, 0% used [0x00000007c71e0000,0x00000007c71e0000,0x00000007e38f0000)
>>  PSOldGen        total 1399808K, used 704584K [0x0000000700000000, 0x0000000755700000, 0x00000007aaab0000)
>>   object space 1399808K, 50% used [0x0000000700000000,0x000000072b012048,0x0000000755700000)
>>  PSPermGen       total 21248K, used 6322K [0x00000006fae00000, 0x00000006fc2c0000, 0x0000000700000000)
>>   object space 21248K, 29% used [0x00000006fae00000,0x00000006fb42c998,0x00000006fc2c0000)
>> 
>> 2011-11-26 01:22:33
>> Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.2-b06 mixed mode):
>> 
>> "Thread-0" prio=10 tid=0x00007f93d818f800 nid=0x1e3f waiting on condition [0x00007f93c5d2f000]
>>    java.lang.Thread.State: WAITING (parking)
>> 	at sun.misc.Unsafe.park(Native Method)
>> 	- parking to wait for<0x0000000700006768>  (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
>> 	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:156)
>> 	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
>> 	at java.util.concurrent.ArrayBlockingQueue.put(ArrayBlockingQueue.java:252)
>> 	at net.sf.picard.sam.MergeSamFiles$1.run(MergeSamFiles.java:155)
>> 	at java.lang.Thread.run(Thread.java:662)
>> 
>> "Low Memory Detector" daemon prio=10 tid=0x00007f93d80c9000 nid=0x1e39 runnable [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "C2 CompilerThread1" daemon prio=10 tid=0x00007f93d80c7000 nid=0x1e38 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "C2 CompilerThread0" daemon prio=10 tid=0x00007f93d80c4000 nid=0x1e37 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "Signal Dispatcher" daemon prio=10 tid=0x00007f93d80c2000 nid=0x1e36 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "Finalizer" daemon prio=10 tid=0x00007f93d80a5800 nid=0x1e35 in Object.wait() [0x00007f93c644c000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
>> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
>> 	- locked<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
>> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
>> 	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
>> 
>> "Reference Handler" daemon prio=10 tid=0x00007f93d80a3800 nid=0x1e34 in Object.wait() [0x00007f93c654d000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>> 	at java.lang.Object.wait(Object.java:485)
>> 	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
>> 	- locked<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>> 
>> "main" prio=10 tid=0x00007f93d8006800 nid=0x1e25 in Object.wait() [0x00007f93dcc9f000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x0000000700024c20>  (a java.lang.Thread)
>> 	at java.lang.Thread.join(Thread.java:1186)
>> 	- locked<0x0000000700024c20>  (a java.lang.Thread)
>> 	at java.lang.Thread.join(Thread.java:1239)
>> 	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:190)
>> 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
>> 	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:84)
>> 
>> "VM Thread" prio=10 tid=0x00007f93d809d000 nid=0x1e33 runnable
>> 
>> "GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f93d8019800 nid=0x1e26 runnable
>> 
>> "GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f93d801b800 nid=0x1e27 runnable
>> 
>> "GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f93d801d800 nid=0x1e28 runnable
>> 
>> "GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f93d801f000 nid=0x1e29 runnable
>> 
>> "GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f93d8021000 nid=0x1e2a runnable
>> 
>> "GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f93d8023000 nid=0x1e2b runnable
>> 
>> "GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f93d8024800 nid=0x1e2c runnable
>> 
>> "GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f93d8026800 nid=0x1e2d runnable
>> 
>> "GC task thread#8 (ParallelGC)" prio=10 tid=0x00007f93d8028000 nid=0x1e2e runnable
>> 
>> "GC task thread#9 (ParallelGC)" prio=10 tid=0x00007f93d802a000 nid=0x1e2f runnable
>> 
>> "GC task thread#10 (ParallelGC)" prio=10 tid=0x00007f93d802c000 nid=0x1e30 runnable
>> 
>> "GC task thread#11 (ParallelGC)" prio=10 tid=0x00007f93d802d800 nid=0x1e31 runnable
>> 
>> "GC task thread#12 (ParallelGC)" prio=10 tid=0x00007f93d802f800 nid=0x1e32 runnable
>> 
>> "VM Periodic Task Thread" prio=10 tid=0x00007f93d80dc000 nid=0x1e3a waiting on condition
>> 
>> JNI global references: 1074
>> 
>> Heap
>>  PSYoungGen      total 932096K, used 17959K [0x00000007aaab0000, 0x0000000800000000, 0x0000000800000000)
>>   eden space 466112K, 3% used [0x00000007aaab0000,0x00000007abc39d90,0x00000007c71e0000)
>>   from space 465984K, 0% used [0x00000007e38f0000,0x00000007e38f0000,0x0000000800000000)
>>   to   space 465984K, 0% used [0x00000007c71e0000,0x00000007c71e0000,0x00000007e38f0000)
>>  PSOldGen        total 1399808K, used 704584K [0x0000000700000000, 0x0000000755700000, 0x00000007aaab0000)
>>   object space 1399808K, 50% used [0x0000000700000000,0x000000072b012048,0x0000000755700000)
>>  PSPermGen       total 21248K, used 6322K [0x00000006fae00000, 0x00000006fc2c0000, 0x0000000700000000)
>>   object space 21248K, 29% used [0x00000006fae00000,0x00000006fb42c998,0x00000006fc2c0000)
>> 
>> 2011-11-26 01:22:43
>> Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.2-b06 mixed mode):
>> 
>> "Thread-0" prio=10 tid=0x00007f93d818f800 nid=0x1e3f waiting on condition [0x00007f93c5d2f000]
>>    java.lang.Thread.State: WAITING (parking)
>> 	at sun.misc.Unsafe.park(Native Method)
>> 	- parking to wait for<0x0000000700006768>  (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
>> 	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:156)
>> 	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
>> 	at java.util.concurrent.ArrayBlockingQueue.put(ArrayBlockingQueue.java:252)
>> 	at net.sf.picard.sam.MergeSamFiles$1.run(MergeSamFiles.java:155)
>> 	at java.lang.Thread.run(Thread.java:662)
>> 
>> "Low Memory Detector" daemon prio=10 tid=0x00007f93d80c9000 nid=0x1e39 runnable [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "C2 CompilerThread1" daemon prio=10 tid=0x00007f93d80c7000 nid=0x1e38 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "C2 CompilerThread0" daemon prio=10 tid=0x00007f93d80c4000 nid=0x1e37 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "Signal Dispatcher" daemon prio=10 tid=0x00007f93d80c2000 nid=0x1e36 waiting on condition [0x0000000000000000]
>>    java.lang.Thread.State: RUNNABLE
>> 
>> "Finalizer" daemon prio=10 tid=0x00007f93d80a5800 nid=0x1e35 in Object.wait() [0x00007f93c644c000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
>> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
>> 	- locked<0x000000070001eb60>  (a java.lang.ref.ReferenceQueue$Lock)
>> 	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
>> 	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
>> 
>> "Reference Handler" daemon prio=10 tid=0x00007f93d80a3800 nid=0x1e34 in Object.wait() [0x00007f93c654d000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>> 	at java.lang.Object.wait(Object.java:485)
>> 	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
>> 	- locked<0x000000070001eaf8>  (a java.lang.ref.Reference$Lock)
>> 
>> "main" prio=10 tid=0x00007f93d8006800 nid=0x1e25 in Object.wait() [0x00007f93dcc9f000]
>>    java.lang.Thread.State: WAITING (on object monitor)
>> 	at java.lang.Object.wait(Native Method)
>> 	- waiting on<0x0000000700024c20>  (a java.lang.Thread)
>> 	at java.lang.Thread.join(Thread.java:1186)
>> 	- locked<0x0000000700024c20>  (a java.lang.Thread)
>> 	at java.lang.Thread.join(Thread.java:1239)
>> 	at net.sf.picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:190)
>> 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
>> 	at net.sf.picard.sam.MergeSamFiles.main(MergeSamFiles.java:84)
>> 
>> "VM Thread" prio=10 tid=0x00007f93d809d000 nid=0x1e33 runnable
>> 
>> "GC task thread#0 (ParallelGC)" prio=10 tid=0x00007f93d8019800 nid=0x1e26 runnable
>> 
>> "GC task thread#1 (ParallelGC)" prio=10 tid=0x00007f93d801b800 nid=0x1e27 runnable
>> 
>> "GC task thread#2 (ParallelGC)" prio=10 tid=0x00007f93d801d800 nid=0x1e28 runnable
>> 
>> "GC task thread#3 (ParallelGC)" prio=10 tid=0x00007f93d801f000 nid=0x1e29 runnable
>> 
>> "GC task thread#4 (ParallelGC)" prio=10 tid=0x00007f93d8021000 nid=0x1e2a runnable
>> 
>> "GC task thread#5 (ParallelGC)" prio=10 tid=0x00007f93d8023000 nid=0x1e2b runnable
>> 
>> "GC task thread#6 (ParallelGC)" prio=10 tid=0x00007f93d8024800 nid=0x1e2c runnable
>> 
>> "GC task thread#7 (ParallelGC)" prio=10 tid=0x00007f93d8026800 nid=0x1e2d runnable
>> 
>> "GC task thread#8 (ParallelGC)" prio=10 tid=0x00007f93d8028000 nid=0x1e2e runnable
>> 
>> "GC task thread#9 (ParallelGC)" prio=10 tid=0x00007f93d802a000 nid=0x1e2f runnable
>> 
>> "GC task thread#10 (ParallelGC)" prio=10 tid=0x00007f93d802c000 nid=0x1e30 runnable
>> 
>> "GC task thread#11 (ParallelGC)" prio=10 tid=0x00007f93d802d800 nid=0x1e31 runnable
>> 
>> "GC task thread#12 (ParallelGC)" prio=10 tid=0x00007f93d802f800 nid=0x1e32 runnable
>> 
>> "VM Periodic Task Thread" prio=10 tid=0x00007f93d80dc000 nid=0x1e3a waiting on condition
>> 
>> JNI global references: 1074
>> 
>> Heap
>>  PSYoungGen      total 932096K, used 17959K [0x00000007aaab0000, 0x0000000800000000, 0x0000000800000000)
>>   eden space 466112K, 3% used [0x00000007aaab0000,0x00000007abc39d90,0x00000007c71e0000)
>>   from space 465984K, 0% used [0x00000007e38f0000,0x00000007e38f0000,0x0000000800000000)
>>   to   space 465984K, 0% used [0x00000007c71e0000,0x00000007c71e0000,0x00000007e38f0000)
>>  PSOldGen        total 1399808K, used 704584K [0x0000000700000000, 0x0000000755700000, 0x00000007aaab0000)
>>   object space 1399808K, 50% used [0x0000000700000000,0x000000072b012048,0x0000000755700000)
>>  PSPermGen       total 21248K, used 6322K [0x00000006fae00000, 0x00000006fc2c0000, 0x0000000700000000)
>>   object space 21248K, 29% used [0x00000006fae00000,0x00000006fb42c998,0x00000006fc2c0000)
>> 
>> Has this behavior been seen by others? Any help would be greatly appreciated.
>> 
>> Here is how I am running it (in this case I am only inputting 1 file so it should just sort the bam file):
>> 
>> java -Xmx4g -Djava.io.tmpdir=/data/tmp -jar /usr/local/picard/Current_jars/MergeSamFiles.jar TMP_DIR=/storage/tmp/QGwNHb6nck MAX_RECORDS_IN_RAM=1000000 I=/storage/tmp/QGwNHb6nck/778Input_TGAT_L008.bam O=/data/pipeline_in/Runs/111027_SN1055_0074_BD0F9GACXX/ProjectFolders/Project_Dale-Garsed/Sample_778Input/Alignment_778Input/778Input_aligned.bam VALIDATION_STRINGENCY=LENIENT SO=coordinate USE_THREADING=true CREATE_INDEX=true>>  /data/pipeline_in/Runs/111027_SN1055_0074_BD0F9GACXX/ProjectFolders/Project_Dale-Garsed/Sample_778Input/Alignment_778Input/Aligner.log 2>&1
>> 
>> thanks,
>> 
>> Jason
>> 
>> 
>> This email (including any attachments or links) may contain
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>> intended only to be read or used by the addressee.  If you
>> are not the intended addressee, any use, distribution,
>> disclosure or copying of this email is strictly
>> prohibited.
>> Confidentiality and legal privilege attached to this email
>> (including any attachments) are not waived or lost by
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>> and notify us immediately by telephone or email.  Peter
>> MacCallum Cancer Centre provides no guarantee that this
>> transmission is free of virus or that it has not been
>> intercepted or altered and will not be liable for any delay
>> in its receipt.
>> 
>> 
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> Samtools-help mailing list
>> Samtools-help@...
>> https://lists.sourceforge.net/lists/listinfo/samtools-help

This email (including any attachments or links) may contain 
confidential and/or legally privileged information and is 
intended only to be read or used by the addressee.  If you 
are not the intended addressee, any use, distribution, 
disclosure or copying of this email is strictly 
prohibited.  
Confidentiality and legal privilege attached to this email 
(including any attachments) are not waived or lost by 
reason of its mistaken delivery to you.
If you have received this email in error, please delete it 
and notify us immediately by telephone or email.  Peter 
MacCallum Cancer Centre provides no guarantee that this 
transmission is free of virus or that it has not been 
intercepted or altered and will not be liable for any delay 
in its receipt.

The ensembl variant effect predictor takes in vcf

http://www.ensembl.org/info/docs/variation/vep/index.html

Laura

On Mon, Nov 28, 2011 at 10:17 PM, Joseph Fass <joseph.fass@...> wrote:
> snpEff is one (http://snpeff.sourceforge.net/), also Annovar ... both should
> work with only gff (i.e. no external database like UCSC, etc)
> ~Joe
>
>
>
> On Fri, Nov 18, 2011 at 1:16 AM, sutada Mungpakdee <msutada@...>
> wrote:
>>
>> Hi,
>>
>> After get SNP calling in vcf format, I would like to annotate SNP, Anyone
>> has a good suggestion about software to try. I'm working with new organism
>> so I have gene annotation file in gff, snp file in vcf. Any suggestion will
>> be great.
>>
>> Best regards,
>> Sutada
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> Samtools-help mailing list
>> Samtools-help@...
>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
>
> --
> Joseph Fass
> Bioinformatics Programmer
> UC Davis Bioinformatics Core
> joseph.fass -at- gmail.com (professional)
> 970.227.5928 (c)  ||  530.752.2698 (w)
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@...
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>

Hi Sutada

Its always best to email the list with these questions

I don't know if any of the other functional tools work on gff as input
as oppose to existing databases

thanks

Laura

On Wed, Nov 30, 2011 at 8:58 AM, sutada Mungpakdee <msutada@...> wrote:
> Hi Laura,
>
> thank you very much for suggestion.
>
> Seem ensembl variant effect predictor works only with known genome. Do you have any suggestion for new organism? I have gene annotation file in gff3.
>
> Best regards,
> Sutada
>
>
> On Nov 29, 2011, at 7:25 AM, Laura Clarke wrote:
>
>> The ensembl variant effect predictor takes in vcf
>>
>> http://www.ensembl.org/info/docs/variation/vep/index.html
>>
>> Laura
>>
>> On Mon, Nov 28, 2011 at 10:17 PM, Joseph Fass <joseph.fass@...> wrote:
>>> snpEff is one (http://snpeff.sourceforge.net/), also Annovar ... both should
>>> work with only gff (i.e. no external database like UCSC, etc)
>>> ~Joe
>>>
>>>
>>>
>>> On Fri, Nov 18, 2011 at 1:16 AM, sutada Mungpakdee <msutada@...>
>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> After get SNP calling in vcf format, I would like to annotate SNP, Anyone
>>>> has a good suggestion about software to try. I'm working with new organism
>>>> so I have gene annotation file in gff, snp file in vcf. Any suggestion will
>>>> be great.
>>>>
>>>> Best regards,
>>>> Sutada
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All the data continuously generated in your IT infrastructure
>>>> contains a definitive record of customers, application performance,
>>>> security threats, fraudulent activity, and more. Splunk takes this
>>>> data and makes sense of it. IT sense. And common sense.
>>>> http://p.sf.net/sfu/splunk-novd2d
>>>> _______________________________________________
>>>> Samtools-help mailing list
>>>> Samtools-help@...
>>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>>
>>>
>>>
>>> --
>>> Joseph Fass
>>> Bioinformatics Programmer
>>> UC Davis Bioinformatics Core
>>> joseph.fass -at- gmail.com (professional)
>>> 970.227.5928 (c)  ||  530.752.2698 (w)
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> _______________________________________________
>>> Samtools-help mailing list
>>> Samtools-help@...
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