GBS pipeline

[Plant Breeding - PBG]

Dear All

I need your help 

I have GBS data from barley. I downloaded a reference genome from ftp://ftp.ensemblgenomes.org/pub/plants/release-32/fasta/hordeum_vulgare/dna/

the extension of reference genome is fa.gz. 

I tried to use this command 

run_pipeline.pl -Xmx512m -fork1 -FastqToTagCountPlugin -i reads/ -k barcode/BarleyKey.csv -e PstI-MspI -m topm/Hordeum_vulgare.ASM32608v1.dna_sm.toplevel.fa.gz -o hapmapout/productionv2_2hmp.h5 -endPlugin -runfork1

i got an error on out. files 

[main] ERROR net.maizegenetics.plugindef.AbstractPlugin - Unrecognized argument: -m

how can I deal with fa.gz if it is a reference genome

Thanks in advance

Ahmed

[Terry Casstevens]

The usage for FastqToTagCountPlugin is below, although you may
consider using the latest TASSEL 5 GBSv2

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline


./run_pipeline.pl -FastqToTagCountPlugin

./lib/ahocorasick-0.2.4.jar:./lib/batik-awt-util.jar:./lib/batik-css.jar:./lib/batik-dom.jar:./lib/batik-ext.jar:./lib/batik-gui-util.jar:./lib/batik-gvt.jar:./lib/batik-parser.jar:./lib/batik-svg-dom.jar:./lib/batik-svggen.jar:./lib/batik-util.jar:./lib/batik-xml.jar:./lib/biojava-alignment-4.0.0.jar:./lib/biojava-core-4.0.0.jar:./lib/biojava-phylo-4.0.0.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/colt.jar:./lib/commons-codec-1.10.jar:./lib/commons-math3-3.4.1.jar:./lib/ejml-0.23.jar:./lib/forester_1034.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/guava-19.0.jar:./lib/htsjdk-1.138.jar:./lib/itextpdf-5.1.0.jar:./lib/javax.json-1.0.4.jar:./lib/jcommon-1.0.6.jar:./lib/je-6.0.11.jar:./lib/jfreechart-1.0.3.jar:./lib/jfxrt.jar:./lib/json-simple-1.1.1.jar:./lib/junit-4.10.jar:./lib/log4j-1.2.13.jar:./lib/mail-1.4.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/slf4j-api-1.7.10.jar:./lib/slf4j-simple-1.7.10.jar:./lib/snappy-java-1.1.1.6.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/trove-3.0.3.jar:./lib/xercesImpl.jar:./lib/xml.jar:./lib/xmlParserAPIs.jar:./dist/sTASSEL.jar

Memory Settings: -Xms512m -Xmx1536m

Tassel Pipeline Arguments: -FastqToTagCountPlugin

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version:
5.2.30 Date: September 1, 2016

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available
Memory Reported by JVM: 1365 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel
Pipeline Arguments: [-fork1, -FastqToTagCountPlugin, -runfork1]

net.maizegenetics.analysis.gbs.FastqToTagCountPlugin

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
Starting net.maizegenetics.analysis.gbs.FastqToTagCountPlugin: time:
Oct 17, 2016 20:56:58

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin -
-i is required.


[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

Usage:

FastqToTagCountPlugin <options>

-i <Input Directory> : Input directory containing FASTQ files in text
or gzipped text. NOTE: Directory will be searched recursively and
should be written WITHOUT a slash after its name. (required)

-k <Key File> : Key file listing barcodes distinguishing the samples (required)

-e <Enzyme> : Enzyme used to create the GBS library, if it differs
from the one listed in the key file (required)

-s <Max Good Reads> : Max good reads per lane (Default: 300000000)

-c <Min Tag Count> : Minimum tag count (Default: 1)

-o <Output Directory> : Output directory to contain .cnt files (one
per FASTQ file (one per FASTQ file) (required)

> --
> You received this message because you are subscribed to the Google Groups
> "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to tassel+un...@googlegroups.com.
> To post to this group, send email to tas...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/tassel/6e949d87-c8c0-4f2a-8930-da4007c63749%40googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

[Plant Breeding - PBG]

Hi Terry 

Thank you for your reply. Actually I am a beginner. I am not sure if I used the correct command -FastqToTagCountPlugin or not. My goal is to a SNP calling for my data. The extension file in the maize reference genome is topm.h5. The reference genome which I found for barley with file extension of fa.gz. I used this command 

run_pipeline.pl -Xmx512m -fork1 -ProductionSNPCallerPlugin -i reads/ -k barcode/BarleyKey.csv -e PstI-MspI -m topm/Hordeum_vulgare.ASM32608v1.dna_sm.toplevel.fa.gz -o hapmapout/productionv2_2hmp.h5 -endPlugin -runfork1

I got this (see Error message)

/util/opt/tassel/5x/lib/biojava3-alignment-3.0.jar:/util/opt/tassel/5x/lib/mail-1.4.jar:/util/opt/tassel/5x/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/util/opt/tassel/5x/lib/geronimo-spec-activation-1.0.2-rc4.jar:/util/opt/tassel/5x/lib/xmlParserAPIs.jar:/util/opt/tassel/5x/lib/log4j-1.2.13.jar:/util/opt/tassel/5x/lib/batik-gvt.jar:/util/opt/tassel/5x/lib/ejml-0.23.jar:/util/opt/tassel/5x/lib/biojava3-core-3.0.jar:/util/opt/tassel/5x/lib/json-simple-1.1.1.jar:/util/opt/tassel/5x/lib/batik-svg-dom.jar:/util/opt/tassel/5x/lib/batik-parser.jar:/util/opt/tassel/5x/lib/batik-css.jar:/util/opt/tassel/5x/lib/biojava3-phylo-3.0.jar:/util/opt/tassel/5x/lib/batik-util.jar:/util/opt/tassel/5x/lib/jfreechart-1.0.3.jar:/util/opt/tassel/5x/lib/batik-xml.jar:/util/opt/tassel/5x/lib/batik-dom.jar:/util/opt/tassel/5x/lib/colt.jar:/util/opt/tassel/5x/lib/forester.jar:/util/opt/tassel/5x/lib/poi-3.0.1-FINAL-20070705.jar:/util/opt/tassel/5x/lib/xml.jar:/util/opt/tassel/5x/lib/itextpdf-5.1.0.jar:/util/opt/tassel/5x/lib/LiuExt.jar:/util/opt/tassel/5x/lib/batik-awt-util.jar:/util/opt/tassel/5x/lib/jcommon-1.0.6.jar:/util/opt/tassel/5x/lib/batik-ext.jar:/util/opt/tassel/5x/lib/batik-svggen.jar:/util/opt/tassel/5x/lib/junit-4.10.jar:/util/opt/tassel/5x/lib/batik-gui-util.jar:/util/opt/tassel/5x/lib/commons-math-2.2.jar:/util/opt/tassel/5x/lib/xercesImpl.jar:/util/opt/tassel/5x/lib/guava-14.0.1.jar:/util/opt/tassel/5x/sTASSEL.jar

Memory Settings: -Xms512m -Xmx512m

Tassel Pipeline Arguments: -fork1 -ProductionSNPCallerPlugin -i reads/ -k barcode/BarleyKey.csv -e PstI-MspI -m topm/Hordeum_vulgare.ASM32608v1.dna_sm.toplevel.fa.gz -o hapmapout/productionv2_2hmp.h5 -endPlugin -runfork1

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 5.1.0  Date: August 28, 2014

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Max Available Memory Reported by JVM: 491 MB

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Java Version: 1.8.0_102

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -ProductionSNPCallerPlugin, -i, reads/, -k, barcode/BarleyKey.csv, -e, PstI-MspI, -m, topm/Hordeum_vulgare.ASM32608v1.dna_sm.toplevel.fa.gz, -o, hapmapout/productionv2_2hmp.h5, -endPlugin, -runfork1]

net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin

[Thread-0] INFO net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin - 

ProductionSNPCallerPlugin:

The following GBS raw sequence data files were found in the input folder (and sub-folders):

   /lustre/work/baenziger/amsallam/GBS/reads/C8R3MACXX_3_.fq.gz

[Thread-0] ERROR net.maizegenetics.plugindef.AbstractPlugin - TOPMUtils: readTOPM: Unknown file extension: topm/Hordeum_vulgare.ASM32608v1.dna_sm.toplevel.fa.gz

[Thread-0] INFO net.maizegenetics.plugindef.AbstractPlugin - 

Usage:

ProductionSNPCallerPlugin <options>

-i <Input Directory> : Input directory containing fastq AND/OR qseq files. (required)

-k <Key File> : Key file listing barcodes distinguishing the samples (required)

-e <Enzyme> : Enzyme used to create the GBS library (required)

-m <Input TOPM File> : Physical map file containing tags and corresponding variants (production TOPM) (required)

-o <Output HDF5 Genotypes File> : Output (target) HDF5 genotypes file to add new genotypes to (new file created if it doesn't exist) (required)

-eR <Ave Seq Error Rate> : Average sequencing error rate per base (used to decide between heterozygous and homozygous calls) (Default: 0.01)

-d <Max Divergence> : Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only) (Default: 0)

-ko <true | false> : Keep hdf5 genotypes open for future runs that add more taxa or more depth (Default: false)

-ndo <true | false> : No depth output: do not write depths to the output hdf5 genotypes file (Default: false)

So, any idea how can tassel read my genome reference with an extension of fa.gz

Thank you for your efforts

Ahmed

[Terry Casstevens]

Your installation of TASSEL is over 2 years old. Can you update that?

Have you read the link that I sent?

Best,

Terry

> --
> You received this message because you are subscribed to the Google Groups
> "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to tassel+un...@googlegroups.com.
> To post to this group, send email to tas...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/tassel/d51045ae-d408-4eb3-8ce2-27e03d68b7e4%40googlegroups.com.

[Ahmed Sallam]

Hi Terry

Thanks. I am using GBSv2 pipeline.

When wrote 

run_pipeline.pl -Xms10G -Xmx20G -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i reads/ -db out/GBSV2.db -k barcode/BarleyKey.csv  -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1

I did not find the GBSV2.db in the out foler and I did not get any error message from running this command. Kindly see below

/util/opt/tassel/5.2/lib/postgresql-9.4-1201.jdbc41.jar:/util/opt/tassel/5.2/lib/commons-codec-1.10.jar:/util/opt/tassel/5.2/lib/slf4j-simple-1.7.10.jar:/util/opt/tassel/5.2/lib/trove-3.0.3.jar:/util/opt/tassel/5.2/lib/jfreechart-1.0.3.jar:/util/opt/tassel/5.2/lib/htsjdk-1.138.jar:/util/opt/tassel/5.2/lib/javax.json-1.0.4.jar:/util/opt/tassel/5.2/lib/log4j-1.2.13.jar:/util/opt/tassel/5.2/lib/batik-css.jar:/util/opt/tassel/5.2/lib/jcommon-1.0.6.jar:/util/opt/tassel/5.2/lib/batik-xml.jar:/util/opt/tassel/5.2/lib/biojava-alignment-4.0.0.jar:/util/opt/tassel/5.2/lib/batik-dom.jar:/util/opt/tassel/5.2/lib/snappy-java-1.1.1.6.jar:/util/opt/tassel/5.2/lib/geronimo-spec-activation-1.0.2-rc4.jar:/util/opt/tassel/5.2/lib/sqlite-jdbc-3.8.5-pre1.jar:/util/opt/tassel/5.2/lib/batik-ext.jar:/util/opt/tassel/5.2/lib/mail-1.4.jar:/util/opt/tassel/5.2/lib/xercesImpl.jar:/util/opt/tassel/5.2/lib/batik-svg-dom.jar:/util/opt/tassel/5.2/lib/slf4j-api-1.7.10.jar:/util/opt/tassel/5.2/lib/poi-3.0.1-FINAL-20070705.jar:/util/opt/tassel/5.2/lib/junit-4.10.jar:/util/opt/tassel/5.2/lib/json-simple-1.1.1.jar:/util/opt/tassel/5.2/lib/biojava-phylo-4.0.0.jar:/util/opt/tassel/5.2/lib/batik-svggen.jar:/util/opt/tassel/5.2/lib/biojava-core-4.0.0.jar:/util/opt/tassel/5.2/lib/guava-14.0.1.jar:/util/opt/tassel/5.2/lib/ahocorasick-0.2.4.jar:/util/opt/tassel/5.2/lib/colt.jar:/util/opt/tassel/5.2/lib/xmlParserAPIs.jar:/util/opt/tassel/5.2/lib/batik-awt-util.jar:/util/opt/tassel/5.2/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/util/opt/tassel/5.2/lib/batik-parser.jar:/util/opt/tassel/5.2/lib/itextpdf-5.1.0.jar:/util/opt/tassel/5.2/lib/batik-util.jar:/util/opt/tassel/5.2/lib/commons-math3-3.4.1.jar:/util/opt/tassel/5.2/lib/xml.jar:/util/opt/tassel/5.2/lib/forester.jar:/util/opt/tassel/5.2/lib/batik-gvt.jar:/util/opt/tassel/5.2/lib/ejml-0.23.jar:/util/opt/tassel/5.2/lib/batik-gui-util.jar:/util/opt/tassel/5.2/sTASSEL.jar

Memory Settings: -Xms10G -Xmx20G

Tassel Pipeline Arguments: -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i reads/ -db out/GBSV2.db -k barcode/BarleyKey.csv -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.25  Date: April 28, 2016

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 18204 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_102

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -GBSSeqToTagDBPlugin, -e, PstI-MspI, -i, reads/, -db, out/GBSV2.db, -k, barcode/BarleyKey.csv, -kmerLength, 64, -minKmerL, 20, -mnQS, 20, -mxKmerNum, 100000000, -endPlugin, -runfork1]

net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Oct 20, 2016 20:39:15

Enzyme: PstI-MspI

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 

GBSSeqToTagDBPlugin Parameters

i: reads/

k: barcode/BarleyKey.csv

e: PstI-MspI

kmerLength: 64

minKmerL: 20

c: 10

db: out/GBSV2.db

mnQS: 20

mxKmerNum: 100000000

batchSize: 8

deleteOldData: true

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Oct 20, 2016 20:39:16

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: Oct 20, 2016 20:39:16: progress: 100%

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

Any recommendations?

Regards

Ahmed

[Lynn Carol Johnson]

Please run in debug mode and send the results.

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Thanks - Lynn

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/68c1ae1f-0ba4-4ba0-a481-a307b8af294d%40googlegroups.com.

[Ahmed Sallam]

Hi Lynn

Thanks for your reply. Kindly find  the attachment

Regards

Ahmed

[Lynn Carol Johnson]

Did you run the plugin?  The debug doesn’t show your command execution.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/4adb1f28-3fa4-4042-8595-8e09faa83ecd%40googlegroups.com.

[Ahmed Sallam]

is that what you need?

[amsa...@login.crane tassel-5-standalone]$ ./run_pipeline.pl ­debug bug/debug

./lib/batik-xml.jar:./lib/batik-dom.jar:./lib/xmlParserAPIs.jar:./lib/junit-4.10.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/snappy-java-1.1.1.6.jar:./lib/json-simple-1.1.1.jar:./lib/batik-css.jar:./lib/trove-3.0.3.jar:./lib/ahocorasick-0.2.4.jar:./lib/guava-19.0.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/batik-gvt.jar:./lib/javax.json-1.0.4.jar:./lib/xercesImpl.jar:./lib/jfreechart-1.0.3.jar:./lib/biojava-core-4.0.0.jar:./lib/batik-svg-dom.jar:./lib/xml.jar:./lib/colt.jar:./lib/biojava-phylo-4.0.0.jar:./lib/log4j-1.2.13.jar:./lib/batik-gui-util.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/biojava-alignment-4.0.0.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/ejml-0.23.jar:./lib/commons-codec-1.10.jar:./lib/batik-svggen.jar:./lib/forester.jar:./lib/batik-parser.jar:./lib/batik-ext.jar:./lib/itextpdf-5.1.0.jar:./lib/batik-awt-util.jar:./lib/mail-1.4.jar:./lib/htsjdk-1.138.jar:./lib/batik-util.jar:./lib/jcommon-1.0.6.jar:./lib/slf4j-api-1.7.10.jar:./lib/slf4j-simple-1.7.10.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/commons-math3-3.4.1.jar:./sTASSEL.jar

Memory Settings: -Xms512m -Xmx1536m

Tassel Pipeline Arguments: ­debug bug/debug

Exception in thread "main" java.lang.UnsupportedClassVersionError: net/maizegenetics/pipeline/TasselPipeline : Unsupported major.minor version 52.0

        at java.lang.ClassLoader.defineClass1(Native Method)

        at java.lang.ClassLoader.defineClass(ClassLoader.java:803)

        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)

        at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)

        at java.net.URLClassLoader.access$100(URLClassLoader.java:71)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:425)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:358)

        at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

[Terry Casstevens]

You need Java 8 to run TASSEL 5

> https://groups.google.com/d/msgid/tassel/9a5501b6-cbdc-46cd-9ee7-12070166f59f%40googlegroups.com.

[Ahmed Sallam]

ok so the problem is not have Java 8. is it right?

Ahmed

[Terry Casstevens]

yes, type

java -version

> https://groups.google.com/d/msgid/tassel/7310cba0-f6e5-4a95-930f-516bbcbf0e41%40googlegroups.com.

[Lynn Carol Johnson]

Correct.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/7310cba0-f6e5-4a95-930f-516bbcbf0e41%40googlegroups.com.

[Lynn Carol Johnson]

Your command line does not look correct.  You added the debug option, but I don’t see where you called a plugin. 

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/9a5501b6-cbdc-46cd-9ee7-12070166f59f%40googlegroups.com.

[Ahmed Sallam]

Hi Lynn

I am a beginner. So, I followed the file that you sent to me.Do you mean instead of writing debug, I should write ./run_pipeline.pl plugin bug/debug. Before that I should run Java/8

Thank you for your patient. I do appreciate your and Terry efforts

Ahmed

[Lynn Carol Johnson]

 Run it as show below, replacing “debugFile” with whatever you want your debug file to be called.  Include directory if appropriate.

run_pipeline.pl -debug debugFile -Xms10G -Xmx20G -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i reads/ -db out/GBSV2.db -k barcode/BarleyKey.csv  -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin –runfork1

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/56b27e7d-ef13-4bb3-b9c2-20d02fe7397b%40googlegroups.com.

[Ahmed Sallam]

Lynn

I wrote this command 

run_pipeline.pl -debug debug -fork1 -TagExportToFastqPlugin -db out/GBSv2.db -o hapmapout/tagsForAlign.fa.gz -c 1 -endPlugin -runfork1

and I got the file in the attachment. Kindly see it

So, I think debug is the file with .db and should be used in the next command. is that right?

Regards

Ahmed

[Lynn Carol Johnson]

Your output shows you ran TagExportToFastqPlugin.    The first step of the pipeline is to run GBSSeqToTagDBPlugin.  This creates the database.

Please see the wiki here for an explanation of the pipeline commands:

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/b5f76138-55ca-4c99-b735-f967fca3b65e%40googlegroups.com.

[Ahmed Sallam]

Yes, you are correct. I get confused. Thanks.

[Lynn Carol Johnson]

When you run the first step, run it in debug mode as I showed you.  If you have problems, send me the debug output file.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/08de329e-a007-428b-af67-c1dc5d360fb6%40googlegroups.com.

[Ahmed Sallam]

Hi Lynn

the new command is 

run_pipeline.pl -debug debug -Xms10G -Xmx20G -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i reads/ -db out/GBSV2.db -k barcode/BarleyKey.csv  -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1

and see debug. I think this the file that should be used in next command as .db. is this correct?

Best Regards

 

Ahmed Sallam

-------------------------------------------------

Assistant Professor

Department of Genetics

Faculty of Agriculture

Assiut University

71526- Assiut, Egypt

--------------------------------------------------

To unsubscribe from this group and stop receiving emails from it, send an email to tassel+unsubscribe@googlegroups.com.

To post to this group, send email to tas...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/08de329e-a007-428b-af67-c1dc5d360fb6%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to a topic in the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/tassel/Myi1knCocX8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to tassel+unsubscribe@googlegroups.com.

To post to this group, send email to tas...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/D42FB823.203D8%25lcj34%40cornell.edu.

[Lynn Carol Johnson]

The file to be used as the db is the file you named as the db.  In your example, it is out/GBSV2.db.

Did your command run, or did you have problems at the command line?  The debug file shows no indication this command was run.  I expect to see the command line executed, and either its completion or errors.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CAKBbuynR73DdXPY4%3DvqDqEO%2BjZ5xiHfPMxJs%3DPsS1DAXPgDNVg%40mail.gmail.com.

[Ahmed Sallam]

Lynn

What I did was

1- I open tassle>>help>>>logging>>cheked debug leve>>> save file as debug >> I copied it in tassel folder

2- run command

 run_pipeline.pl -debug debug -Xms10G -Xmx20G -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i reads/ -db out/GBSV2.db -k barcode/BarleyKey.csv  -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1

As a result

I did not find any error message and when I opened folder out, i did not find GBSV2.db 

I found debug is changed and sent the debug file to you..

I do not know the where the error is

Thanks

Best Regards

 

Ahmed Sallam

-------------------------------------------------

Assistant Professor

Department of Genetics

Faculty of Agriculture

Assiut University

71526- Assiut, Egypt

--------------------------------------------------

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CAKBbuynR73DdXPY4%3DvqDqEO%2BjZ5xiHfPMxJs%3DPsS1DAXPgDNVg%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to a topic in the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/tassel/Myi1knCocX8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to tassel+unsubscribe@googlegroups.com.
To post to this group, send email to tas...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/D42FC3E7.203DD%25lcj34%40cornell.edu.

[Lynn Carol Johnson]

If you are running from the command line, you do not need to open TASSEL help.  That is for when you are running from the GUI.  Please skip that step.  You are overwriting your actual command run with what is essentially an empty file.

 The debug file you need to send me is the one you created from the command line.  You called it “debug”.  Because you did not indicate a directory it should live in the same folder where you are executing the command.  Please run the command again and send me the debug file created from the command line run.

IS there someone local who can help you understand the basics of running commands?

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CAKBbuynZmY47Pzk5fSt-F7voX7Vbkoh3Cg30JWOcWGi0Frft1Q%40mail.gmail.com.

[Ahmed Sallam]

Lynn

I knew that the debug file will be in the same directory. I run the command using two different ways

1-  run_pipeline.pl -debug debug

kindly see the attachment the file name is debug

2- run_pipeline.pl -debug debug2 -Xms512m -Xmx1536m  -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i reads/ -db out/GBSV2.db -k barcode/BarleyKey.csv  -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1..

kindly see the attachment. the name of file is debug1

Thank you. if you would like I can send your the out files of these commands

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CAKBbuynZmY47Pzk5fSt-F7voX7Vbkoh3Cg30JWOcWGi0Frft1Q%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to a topic in the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/tassel/Myi1knCocX8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to tassel+unsubscribe@googlegroups.com.
To post to this group, send email to tas...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/D4322380.20D0B%25lcj34%40cornell.edu.

[Edward S. Buckler]

I haven't been looking at the debug files yet, but the memory maximum looks very small GBS discovery generally requires many Gbs of RAM.

Cheers-

Ed

Sent from my iPad

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CAKBbuykcbD-kZzu2WRdSeHzB74XJVEXBye4pwwUVsz_-FEi6Lw%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.

<debug>

<debug1>

[Ahmed Sallam]

Thanks for reply. 

I have attached two files. each one was generated by different command. I need to know which one is correct. 

With regard to the memory, our server has memory of 64 GB. When I run command as fellow

run_pipeline.pl -debug debug2 -Xms10g -Xmx20g  -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i reads/ -db out/GBSV2.db -k barcode/BarleyKey.csv  -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1..

kindly see the attachment. the name of file is debug1

it gave me the same results as they are in debug1 file (see attachment)

My main problem that I was not able to find GBSV2.db file in the out folder to use it for the next command. (see command above)

Thanks for all 

Ahmed

[Lynn Carol Johnson]

Your debug file shows no errors, but also that nothing was processed.    Your TASSEL version is from last April.  Since then we’ve added additional error messages.

 If you run with the latest version of tassel-5 I believe you’ll see an error message indicating there were no files found that are represented in the key file.  You should verify your file names are formatted correctly and that your key file contains the required headers.

Please read the wiki page for the GBSv2 pipeline.  Under the FAQ section of the GBSSetToTagDBPlugin page this scenario is addressed.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline/GBSSeqToTagDBPlugin

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/1a337f32-bbb8-4897-a6d0-853661637af3%40googlegroups.com.

[Ahmed Sallam]

Lynn Terry and Edward

Thank you so much for your help. I do appreciate your great efforts to help me. 

I successfully solved the problem and was able to generate .db.

With my best regards

Ahmed