SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to install Bowtie gene_x Bioinformatics 172 08-13-2015 10:58 AM
CASAVA 1.7 Install Help aligenie Bioinformatics 29 05-23-2014 03:58 AM
how to install picard ? eilosei Bioinformatics 4 12-15-2011 08:17 AM
How to install ALLPATHLG? skblazer Bioinformatics 0 01-12-2011 12:59 PM
BFAST - Install Adamo Bioinformatics 4 06-08-2010 01:02 AM

Reply
 
Thread Tools
Old 05-24-2010, 11:22 AM   #1
cliff
Member
 
Location: USA

Join Date: Oct 2009
Posts: 41
Default how to install and use Picard

Dear all,

I want to use Picard to remove PCR duplicates and I downloaded picard-tools-1.21.zip from

http://sourceforge.net/projects/picard/files/

After unzip it in linux, I got these files:

CleanSam.jar CreateSequenceDictionary.jar FastqToSam.jar MergeSamFiles.jar ReplaceSamHeader.jar SamFormatConverter.jar SortSam.jar ViewSam.jar
CompareSAMs.jar EstimateLibraryComplexity.jar MarkDuplicates.jar picard-1.21.jar sam-1.21.jar SamToFastq.jar ValidateSamFile.jar

I am not familar with Java at all and have no idea about what the next step is..

All your help will be greatly appreciated!
cliff is offline   Reply With Quote
Old 05-24-2010, 12:31 PM   #2
kopi-o
Senior Member
 
Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

In general, if you have Java installed, you run jar files like this:

java -jar MarkDuplicates.jar

You may sometimes have to increase the memory available to Java using the -Xmx option. There are also many other options (http://java.sun.com/j2se/1.3/docs/to...aris/java.html)
kopi-o is offline   Reply With Quote
Old 04-19-2012, 12:56 PM   #3
wangli
Member
 
Location: Texas

Join Date: Apr 2012
Posts: 48
Default

[li@raven picard-tools-1.66]$ ls
AddOrReplaceReadGroups.jar CollectMultipleMetrics.jar FixMateInformation.jar ReorderSam.jar
BamIndexStats.jar CollectRnaSeqMetrics.jar IlluminaBasecallsToSam.jar ReplaceSamHeader.jar
BamToBfq.jar CompareSAMs.jar IntervalListTools.jar RevertSam.jar
BuildBamIndex.jar CreateSequenceDictionary.jar MarkDuplicates.jar sam-1.66.jar
CalculateHsMetrics.jar DownsampleSam.jar MeanQualityByCycle.jar SamFormatConverter.jar
CheckIlluminaDirectory.jar EstimateLibraryComplexity.jar MergeBamAlignment.jar SamToFastq.jar
CleanSam.jar ExtractIlluminaBarcodes.jar MergeSamFiles.jar SortSam.jar
CollectAlignmentSummaryMetrics.jar ExtractSequences.jar NormalizeFasta.jar ValidateSamFile.jar
CollectGcBiasMetrics.jar FastqToSam.jar picard-1.66.jar ViewSam.jar
CollectInsertSizeMetrics.jar FilterSamReads.jar QualityScoreDistribution.jar

[li@raven picard-tools-1.66]$ java -Xmx2000m SamToFastq.jar
Exception in thread "main" java.lang.NoClassDefFoundError: SamToFastq/jar
Caused by: java.lang.ClassNotFoundException: SamToFastq.jar
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)

Could not find the main class: SamToFastq.jar. Program will exit.


I am confronted with the above problem when using the picard tool kit.
Any idea? Thanks!
wangli is offline   Reply With Quote
Old 04-19-2012, 01:20 PM   #4
thedamian
Member
 
Location: Barcelona

Join Date: Feb 2012
Posts: 49
Default

Try to provide an Input file an example:
Code:
java -jar SortSam.jar I=/path/input.sam SO=coordinate O=/path/outpu.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
thedamian is offline   Reply With Quote
Old 04-19-2012, 01:43 PM   #5
wangli
Member
 
Location: Texas

Join Date: Apr 2012
Posts: 48
Default

Thanks, thedamian, got it work now!
wangli is offline   Reply With Quote
Old 05-12-2015, 02:34 AM   #6
j6163m
Member
 
Location: Madrid

Join Date: May 2015
Posts: 14
Default Problems with SortSam. jar file (Picard)-My Linux doesn´t find or it has not loaded

Hello, When I try to use last version Picard in my Linux for make this step with my files exome analysis,my computer outputs the next message or similar:

"SortSam.jar file (Picard) is not found or it has not loaded".


I have downloaded last version Picard into my Linux.I have tried to look for the SortSam.jar file into my Picard folders,but I don´t find it.

Somebody could help me,please, so I can go on with my exome analysis?


Waiting for your answers,please,thank you so much.

JM

Last edited by j6163m; 05-12-2015 at 02:37 AM.
j6163m is offline   Reply With Quote
Old 05-12-2015, 02:41 AM   #7
thedamian
Member
 
Location: Barcelona

Join Date: Feb 2012
Posts: 49
Default

maybe try do download older versions and copy SortSam.jar to a new version folder. And maybe then try to execute it from the picard folder - It is just my first guess, don't know if will help
thedamian is offline   Reply With Quote
Old 05-12-2015, 03:05 AM   #8
j6163m
Member
 
Location: Madrid

Join Date: May 2015
Posts: 14
Default

Thank´s thedamian.I will proof it.Can I download older versions from picard web or I must go to another web pages or sites?.Where can I find these older versions picard and this file?

Thank you.

JM
j6163m is offline   Reply With Quote
Old 05-12-2015, 03:09 AM   #9
thedamian
Member
 
Location: Barcelona

Join Date: Feb 2012
Posts: 49
Default

I believe here: http://sourceforge.net/projects/pica.../picard-tools/
thedamian is offline   Reply With Quote
Old 05-12-2015, 03:23 AM   #10
j6163m
Member
 
Location: Madrid

Join Date: May 2015
Posts: 14
Default

Thank you so much.I have just seen the Sortsam.jar file in versión before to last.I will proof it.

JM
j6163m is offline   Reply With Quote
Old 05-12-2015, 10:29 AM   #11
j6163m
Member
 
Location: Madrid

Join Date: May 2015
Posts: 14
Default

Hello again thedamian.I have tried to execute SortSam.jar from the picard folder (after I downloaded and copy to a new version picard folder), but I'm not sure to know do it well.
Could you help me, please and show me the code?.Where I have to place (copy) exactly the SortSam.jar file, in what folder or subfolder belongs to picard folder?.

What I am trying is to execute the next code (step in Exome analysis):

ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~/Escritorio$ java -Xmx4g -Djava.io.tmpdir=/tmp \
> -jar picard/SortSam.jar \
> SO=coordinate \
> INPUT=input.sam \
> OUTPUT=output.bam \
> VALIDATION_STRINGENCY=LENIENT \
> CREATE_INDEX=true
Error: Unable to access jarfile picard/SortSam.jar

But, as you can see above always gives me Error:Unable to access jarfile picard/SortSam.jar

What can I do?.
Waiting for your help, please,thank you so much .

JM
j6163m is offline   Reply With Quote
Old 05-12-2015, 10:53 AM   #12
thedamian
Member
 
Location: Barcelona

Join Date: Feb 2012
Posts: 49
Default

Well, it was my guessing, don't know if will work
anyway, try also:
a) try to use older version of picard
b) try to add picard's folder with .jar files to your env path
c) or use full path to desired .jar

ps. Picard's jar has a parameter TMP_DIR so you can use it instead of -Djava.io.tmpdir (I believe), so the command would be like this:
Quote:
java -Xmx4g -jar /full/path/to/picard/SortSam.jar SO=coordinate INPUT=input.sam OUTPUT=output.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true TMP_DIR=/tmp
thedamian is offline   Reply With Quote
Old 05-12-2015, 03:18 PM   #13
j6163m
Member
 
Location: Madrid

Join Date: May 2015
Posts: 14
Default

I don't get to execute the picard step in my exome analysis.Probably I dont type or write well the path.The output is always:

ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~/Escritorio$ java -Xmx4g -jar /full/path/to/picard/SortSam.jar SO=coordinate INPUT=input.sam OUTPUT=output.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true TMP_DIR=/tmp
Error: Unable to access jarfile /full/path/to/picard/SortSam.jar

I have copied SortSam. jar file in the directory:Escritorio/broadinstitute-picard-60603cd/src/java/picard .But I don t know if this is a right path or location.Thatś right or wrong the location of SortSam.jar file?

I don t know how to solve the problem.

Any idea,please?. Thank you.

JM
j6163m is offline   Reply With Quote
Old 05-13-2015, 02:02 AM   #14
j6163m
Member
 
Location: Madrid

Join Date: May 2015
Posts: 14
Default

Hello thedamian,

When I unzip SortSam.jar file there are 4 folders,one of these is picard.Where I must place or unzip SortSam.jar,in what picard folder (because I see there are several picard folders ,in different locations?

Waiting for your answer,please,Thank you so much

JM
j6163m is offline   Reply With Quote
Old 05-16-2015, 03:49 AM   #15
j6163m
Member
 
Location: Madrid

Join Date: May 2015
Posts: 14
Default

Hello everybody,

Please, somebody could help me with this problem(above) ?.I can not go on with my exome analysis if this problem doesn t solve .

Or another possible solution: Somebody could explain me,please, another different script or method to convert SAM files to BAM files?.

Waiting for your answers,thank you so much for your help.

JM
j6163m is offline   Reply With Quote
Old 05-16-2015, 07:02 AM   #16
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

Quote:
Originally Posted by j6163m View Post
Or another possible solution: Somebody could explain me,please, another different script or method to convert SAM files to BAM files?.
Use samtools to do the conversion: http://davetang.org/wiki/tiki-index...._to_a_BAM_file
GenoMax is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:32 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO