MLM Association error message: The fixed effect design matrix has less than full column rank.

[Hui Zhen Tan]

Hi there,

I am getting this error message when running MLM association: java.lang.IllegalArgumentException: The fixed effect design matrix has less than full column rank. The analysis will not be run. Despite the error message, the expected output files are generated but with some 'NaN' values, usually in the additive and dominant model results columns.

Code

./run_pipeline.pl -debug debug -Xms16g -Xmx30g \
-fork1 -vcf snps.vcf.gz -sortPositions \
-fork2 -r phenotype.txt \
-combine3 -input1 -input2 -intersect \
-fork4 -k kinship.txt \
-combine6 -input3 -input4 \
-mlm \
-mlmOutputFile output-debug \
-mlmCompressionLevel None \
-mlmVarCompEst EachMarker \
-input3 -input4

Input files

1. VCF file: SNPs post-imputation
2. Kinship file: calculated with TASSEL
3. Phenotype file: see snippet below

<Phenotype>
taxa factor factor covariate data
sample cohort sex F_total Total_offspring
1 2005/06 M 0.493554108 15
2 2010/11 F 0.540989274 8
3 2010/11 F 0.53538152 2
4 2012/13 M 0.530213167 4
5 2010/11 F 0.4711944 0
6 2013/14 F 0.47024217 0
7 2010/11 F 0.565642583 0
8 2007/08 F 0.580634868 11

...

Debug file

BuilderFromVCF data timing 8.80502s
Genotype Table Name: dataset
Number of Taxa: 29
Number of Sites: 2820530
Sites x Taxa: 81795370
Chromosomes...
1: start site: 0 (1282) last site: 329481 (99334487) total: 329482
1A: start site: 329482 (341) last site: 543934 (68232092) total: 214453
2: start site: 543935 (951) last site: 1038730 (144383286) total: 494796
3: start site: 1038731 (27451) last site: 1410237 (111862313) total: 371507
4: start site: 1410238 (336) last site: 1651212 (70256115) total: 240975
4A: start site: 1651213 (908) last site: 1704675 (20122219) total: 53463
5: start site: 1704676 (418) last site: 1879628 (61398865) total: 174953
6: start site: 1879629 (106) last site: 1982698 (34921426) total: 103070
7: start site: 1982699 (475) last site: 2110986 (38994402) total: 128288
8: start site: 2110987 (1784) last site: 2192521 (26757560) total: 81535
9: start site: 2192522 (407) last site: 2263609 (25275341) total: 71088
10: start site: 2263610 (20913) last site: 2319755 (20934646) total: 56146
11: start site: 2319756 (3234) last site: 2383306 (21200190) total: 63551
12: start site: 2383307 (400) last site: 2443654 (21201233) total: 60348
13: start site: 2443655 (1847) last site: 2494990 (18349659) total: 51336
14: start site: 2494991 (10941) last site: 2538949 (16674449) total: 43959
15: start site: 2538950 (1425) last site: 2579421 (14339592) total: 40472
17: start site: 2579422 (14036) last site: 2609202 (11209180) total: 29781
18: start site: 2609203 (40) last site: 2642140 (11563475) total: 32938
19: start site: 2642141 (1457) last site: 2665913 (11201901) total: 23773
20: start site: 2665914 (7445) last site: 2702260 (15315810) total: 36347
21: start site: 2702261 (10226) last site: 2719641 (7848977) total: 17381
22: start site: 2719642 (15438) last site: 2735371 (4859117) total: 15730
23: start site: 2735372 (50352) last site: 2750489 (6932200) total: 15118
24: start site: 2750490 (7277) last site: 2769773 (6998634) total: 19284
25A: start site: 2769774 (4801) last site: 2772763 (1995438) total: 2990
25B: start site: 2772764 (4502) last site: 2776199 (1244306) total: 3436
26: start site: 2776200 (495) last site: 2790994 (6659265) total: 14795
27: start site: 2790995 (1168) last site: 2803397 (5745385) total: 12403
28: start site: 2803398 (187) last site: 2816536 (5560862) total: 13139
29: start site: 2816537 (1860) last site: 2820529 (2804130) total: 3993

java.lang.IllegalArgumentException: The fixed effect design matrix has less than full column rank. The analysis will not be run.
at net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix.<init>(EMMAforDoubleMatrix.java:124)
at net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix.testMarkerUsingEMMA(CompressedMLMusingDoubleMatrix.java:802)
at net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix.solve(CompressedMLMusingDoubleMatrix.java:452)
at net.maizegenetics.analysis.association.WeightedMLMPlugin.processData(WeightedMLMPlugin.java:252)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2018)
at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1919)
at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1935)
at net.maizegenetics.analysis.data.CombineDataSetsPlugin.performFunction(CombineDataSetsPlugin.java:65)
at net.maizegenetics.analysis.data.CombineDataSetsPlugin.dataSetReturned(CombineDataSetsPlugin.java:126)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:30)

When I searched the error in this group, I found a thread which suggests that the error might be due to the 0's in the data column of my phenotype file - is that right? Any help on explaining the error would be much appreciated.

Thank you!

Best wishes,

Hui Zhen

[Terry Casstevens]

I think this is usually related to the population structure, and
removing one of the columns from the population structure fixes this.
But it doesn't look like you have a population structure?

> --
> 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 view this discussion visit https://groups.google.com/d/msgid/tassel/1410cd7d-41ca-43ea-9f0f-a23af6bdda6fn%40googlegroups.com.

[Hui Zhen Tan]

Hi Terry,

Yeah I didn't input a population structure file when running TASSEL.

Best wishes,

Hui Zhen

[Hui Zhen Tan]

Some updates to my issue:

 

I have since reran my analyses using the same code and input formats but on 479 individuals (instead of 29 as shown in my initial post). I am still seeing the same error messages but, again, was able to get the expected output files with some 'NaN' values, usually in the additive and dominant model results columns. An example of the output stats.txt file is attached.

 

When the original dataset with 29 individuals was run on GUI, the output files were the same (in terms of values) as what I got from the command line run despite all those error messages.

 

If anyone has encountered this error before and solved it or knows whether getting those error messages and 'NaN' values is detrimental, please let me know. Thank you!

 

Best wishes,

Hui Zhen

[Muhammad Atif Wahid]

i want perform analysis of tassel 2.1 using ssr markers its not running without java

To view this discussion visit https://groups.google.com/d/msgid/tassel/8275550b-3768-492b-ab0e-3b8ee2dc1bdan%40googlegroups.com.

[Terry Casstevens]

Please try updating to the latest version of TASSEL which may have fixed this.

Please follow these instructions to get more information.

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

Best,

Terry

> To view this discussion visit https://groups.google.com/d/msgid/tassel/8275550b-3768-492b-ab0e-3b8ee2dc1bdan%40googlegroups.com.