-UMergeTaxaTagCountPlugin error
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Ashwani Kumar Mishra
Oct 13, 2012, 11:01:57 AM10/13/12
to tas...@googlegroups.com
Hello,
When im executing the following command for merging tag count files i'm getting error, changing the value of c did not change the problem
./run_pipeline.pl -fork1 -UMergeTaxaTagCountPlugin -w M:/UNEAK/ -c 5 -endPlugin -runfork1
Reading Haplotypes distribution from:/data/softwares/tassel3.0_standalone/M:/UNEAK/tagCounts/11C9_151_D17NTACXX_8_250106189.cnt
Number of Tags in file:327387
Reading Haplotypes distribution from:/data/softwares/tassel3.0_standalone/M:/UNEAK/tagCounts/11C9_153_D17NTACXX_8_250106191.cnt
Number of Tags in file:397788
Exception in thread "Thread-0" java.lang.ArrayIndexOutOfBoundsException: 10000000
at net.maizegenetics.gbs.tagdist.TagCountMutable.addReadCounts(TagCountMutable.java:61)
at net.maizegenetics.gbs.pipeline.UMergeTaxaTagCountPlugin.mergeTaxa(UMergeTaxaTagCountPlugin.java:101)
at net.maizegenetics.gbs.pipeline.UMergeTaxaTagCountPlugin.performFunction(UMergeTaxaTagCountPlugin.java:59)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
Any advice on how to fix it?
Best Regards,
Ashwani
Fei Lu
Oct 14, 2012, 12:09:42 AM10/14/12
to tas...@googlegroups.com
Hi Ashwani,
If 11C9_151 or 11C9_153 is a sample name, please remove "_" from the name. You can make this change in key file. UNEAK assumes the string from the start to the first "_" as the sample name. Samples starting with 11C9 would be merged together in this way. It exceeds the tag limit (100,000,000) for each taxa. A large number of this limit would slow down the speed. Let me know if you still have questions.
Best,
Fei Lu
If 11C9_151 or 11C9_153 is a sample name, please remove "_" from the name. You can make this change in key file. UNEAK assumes the string from the start to the first "_" as the sample name. Samples starting with 11C9 would be merged together in this way. It exceeds the tag limit (100,000,000) for each taxa. A large number of this limit would slow down the speed. Let me know if you still have questions.
Best,
Fei Lu
From: tas...@googlegroups.com [tas...@googlegroups.com] on behalf of Ashwani Kumar Mishra [ashwan...@gmail.com]
Sent: Saturday, October 13, 2012 11:01 AM
To: tas...@googlegroups.com
Subject: [TASSEL-Group] -UMergeTaxaTagCountPlugin error
Sent: Saturday, October 13, 2012 11:01 AM
To: tas...@googlegroups.com
Subject: [TASSEL-Group] -UMergeTaxaTagCountPlugin error
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Ashwani Kumar Mishra
Oct 15, 2012, 11:51:06 PM10/15/12
to tas...@googlegroups.com, fl...@cornell.edu
Hi Lu,
Thank you for the suggestion, the problem with progeny filename was solved after renaming them and removing underscores. However the problem still persists with the Parental samples:
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_D04.cnt
Number of Tags in file:557705
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_C08.cnt
Number of Tags in file:549082
Position index sort begin.
Position index sort end.
Position index sort begin.
Position index sort end.
Rows collapsed:1993881
Unique tags retained:7938072
P1Q1 currently contains 7938072 tags.
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_A07.cnt
Number of Tags in file:827606
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_A06.cnt
Number of Tags in file:484258
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_D09.cnt
Number of Tags in file:459987
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_A03.cnt
Number of Tags in file:809086
Exception in thread "Thread-0" java.lang.ArrayIndexOutOfBoundsException: 10000000
at net.maizegenetics.gbs.tagdist.TagCountMutable.addReadCounts(TagCountMutable.java:61)
at net.maizegenetics.gbs.pipeline.UMergeTaxaTagCountPlugin.mergeTaxa(UMergeTaxaTagCountPlugin.java:101)
at net.maizegenetics.gbs.pipeline.UMergeTaxaTagCountPlugin.performFunction(UMergeTaxaTagCountPlugin.java:59)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
There is no underscore or spaces or colons i the sample name now, still ther is this problem.
Best Regards,
Ashwani
Thank you for the suggestion, the problem with progeny filename was solved after renaming them and removing underscores. However the problem still persists with the Parental samples:
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_D04.cnt
Number of Tags in file:557705
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_C08.cnt
Number of Tags in file:549082
Position index sort begin.
Position index sort end.
Position index sort begin.
Position index sort end.
Rows collapsed:1993881
Unique tags retained:7938072
P1Q1 currently contains 7938072 tags.
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_A07.cnt
Number of Tags in file:827606
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_A06.cnt
Number of Tags in file:484258
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_D09.cnt
Number of Tags in file:459987
Reading Haplotypes distribution from:/data/GBS/DS/Phase2/jrb_11c9/uneak/M:/UNEAK/tagCounts/P1Q1_C0L2NACXX_1_Parentslibrary1_A03.cnt
Number of Tags in file:809086
Exception in thread "Thread-0" java.lang.ArrayIndexOutOfBoundsException: 10000000
at net.maizegenetics.gbs.tagdist.TagCountMutable.addReadCounts(TagCountMutable.java:61)
at net.maizegenetics.gbs.pipeline.UMergeTaxaTagCountPlugin.mergeTaxa(UMergeTaxaTagCountPlugin.java:101)
at net.maizegenetics.gbs.pipeline.UMergeTaxaTagCountPlugin.performFunction(UMergeTaxaTagCountPlugin.java:59)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
Best Regards,
Ashwani
Fei Lu
Oct 15, 2012, 11:58:45 PM10/15/12
to Ashwani Kumar Mishra, tas...@googlegroups.com
Hi Ashiwani,
I guess you deep sequenced the parents. What's the estimated genome size? What enzyme? What's the sequence depth?
Best,
Fei
I guess you deep sequenced the parents. What's the estimated genome size? What enzyme? What's the sequence depth?
Best,
Fei
From: Ashwani Kumar Mishra [ashwan...@gmail.com]
Sent: Monday, October 15, 2012 11:51 PM
To: tas...@googlegroups.com
Cc: Fei Lu
Subject: Re: [TASSEL-Group] -UMergeTaxaTagCountPlugin error
Sent: Monday, October 15, 2012 11:51 PM
To: tas...@googlegroups.com
Cc: Fei Lu
Subject: Re: [TASSEL-Group] -UMergeTaxaTagCountPlugin error
Ashwani Kumar Mishra
Oct 16, 2012, 12:14:39 AM10/16/12
to tas...@googlegroups.com, Ashwani Kumar Mishra, fl...@cornell.edu
Hi Lu,
Yes, we deep sequenced the parents.
the estimated genome size of parents is approx 450 MB. We used ApeKI enzyme and we generated approx 6Gb data for each of the parents separately.
Best Regards,
Ashwani
Yes, we deep sequenced the parents.
the estimated genome size of parents is approx 450 MB. We used ApeKI enzyme and we generated approx 6Gb data for each of the parents separately.
Best Regards,
Ashwani
Ashwani Kumar Mishra
Oct 16, 2012, 1:54:52 PM10/16/12
to tas...@googlegroups.com, Ashwani Kumar Mishra, fl...@cornell.edu
Hi Lu,
Any advice on how can we fix this error in UNEAK.
Best Regards,
Ashwani
Any advice on how can we fix this error in UNEAK.
Best Regards,
Ashwani
Fei Lu
Oct 16, 2012, 1:57:16 PM10/16/12
to Ashwani Kumar Mishra, tas...@googlegroups.com
Hi Ashwani,
I will add an user option of the tag limit for each taxa. It will be there on Thursday.
Best,
Fei Lu
I will add an user option of the tag limit for each taxa. It will be there on Thursday.
Best,
Fei Lu
From: Ashwani Kumar Mishra [ashwan...@gmail.com]
Sent: Tuesday, October 16, 2012 1:54 PM
To: tas...@googlegroups.com
Cc: Ashwani Kumar Mishra; Fei Lu
To: tas...@googlegroups.com
Cc: Ashwani Kumar Mishra; Fei Lu
Fei Lu
Oct 17, 2012, 5:44:53 PM10/17/12
to tas...@googlegroups.com, Ashwani Kumar Mishra
Hi Ashwani,
I add a -x option for merging taxa in UMergeTaxaTagCountPlugin. You can set a big enough limit (e.g. -x 10000000) to merge the TagCount files of identical taxa. We will make a new build of Tassel 3 today. So the new option will be available tomorrow. Thanks!
Best,
Fei Lu
I add a -x option for merging taxa in UMergeTaxaTagCountPlugin. You can set a big enough limit (e.g. -x 10000000) to merge the TagCount files of identical taxa. We will make a new build of Tassel 3 today. So the new option will be available tomorrow. Thanks!
Best,
Fei Lu
From: tas...@googlegroups.com [tas...@googlegroups.com] on behalf of Fei Lu [fl...@cornell.edu]
Sent: Tuesday, October 16, 2012 1:57 PM
To: Ashwani Kumar Mishra; tas...@googlegroups.com
Subject: RE: [TASSEL-Group] -UMergeTaxaTagCountPlugin error
Sent: Tuesday, October 16, 2012 1:57 PM
To: Ashwani Kumar Mishra; tas...@googlegroups.com
Subject: RE: [TASSEL-Group] -UMergeTaxaTagCountPlugin error
Hi Ashwani,
I will add an user option of the tag limit for each taxa. It will be there on Thursday.
I will add an user option of the tag limit for each taxa. It will be there on Thursday.
Best,
Fei Lu
Fei Lu
From: Ashwani Kumar Mishra [ashwan...@gmail.com]
Cc: Ashwani Kumar Mishra; Fei Lu
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