search

vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
31 stars 4 forks source link

SKAT errors #138

Open BoPeng opened 4 years ago

BoPeng commented 4 years ago

We are working in a docker station and are using version 3.0.2 of Vtools and version 3.7.2 of Python.

The SKAT test is no longer doable and we get this error message:

Testing for association: 100% [=====================] 102/102 19.7/s in 00:00:05

WARNING: Field sample_size_skat has all missing values

WARNING: No valid integer values has been found for field sample_size_skat

WARNING: Field Q_stats_skat has all missing values

WARNING: No valid float values has been found for field Q_stats_skat

WARNING: Field pvalue_skat has all missing values

WARNING: No valid float values has been found for field pvalue_skat

INFO: Association tests on 102 groups have completed. 102 failed.

INFO: Using annotation DB skat as skat in project asthmaburden.

INFO: Annotation database used to record results of association tests. Created o                                                                                                                                                                                                                                             n Tue, 07 Jan 2020 07:14:55

INFO: 102 out of 25360 refGene.refGene.name2 are annotated through annotation da                                                                                                                                                                                                                                             tabase skat

DEBUG: The first 100 values not annotated are: MIR3130-1, SNX33, UTY, OR8G1, GGC                                                                                                                                                                                                                                             T, NGEF, DEFB115, ANKRD34A, POLL, ATP5L, TEX26, PRKCI, ZCCHC14, MINOS1P1, MIR519                                                                                                                                                                                                                                             4, TOMM70A, FAM25G, CHST14, AOC2, ASS1, OR4A5, NLRP6, OSBPL10-AS1, CCRN4L, MIR31                                                                                                                                                                                                                                             21, HACE1, BANK1, MIR519E, FAM204A, SNORD59B, LINC01021, LOC100507547, PLSCR5, M                                                                                                                                                                                                                                             IR548Z, CC2D2B, WDR63, LARP1, MYO1G, ACO2, CACNA2D3, TWF1, RPS6KA2-IT1, NEO1, EL                                                                                                                                                                                                                                             F4, TMEM108-AS1, MROH6, SPTBN2, KLF4, FXYD3, THOC1, HAAO, RBMY3AP, IFT172, VENTX                                                                                                                                                                                                                                             P7, HNF4A-AS1, ADIPOQ, KIF3B, RNF125, LINC00051, CHRM1, KIR2DL4, FCN2, ALAD, HIS                                                                                                                                                                                                                                             T2H3C, HNRNPLL, FAM95C, OR10H4, SPCS1, OR2A7, TBL1Y, PARD3B, CAMKK1, CCDC184, AA                                                                                                                                                                                                                                             TK, LRRC45, CFL1, CDK6, MT1G, CD99L2, SCNN1A, ORC1, SAP30, PDE12, TTLL13, ITIH1,                                                                                                                                                                                                                                              ARL1, TP73, PLA1A, AP1S2, C8orf86, SYNJ2, GC, PLXND1, LOC101927592, PPP1R2, SPA                                                                                                                                                                                                                                             G5-AS1, DAZAP1, LINC00595, IFT81, ADRA2C

I have tried different versions of Vtools, however I get the same error message over with the different versions. Do you have any suggestions for how we can solve this issue.

BoPeng commented 4 years ago

@gaow Do you on the top of your mind any comment on such warnings? Is it normal or something went wrong?

gaow commented 4 years ago

I think it might have to do with incompatibility with recent SKAT releases (which may not be backwards compatible in terms of interface). It would be best if we upgrade our SKAT test to work with the latest SKAT releases.

BoPeng commented 4 years ago

Just to make sure we are on the same page, could you verify if you could run the following commands?

vtools init skat --parent vt_ExomeAssociation -f
vtools use refGene
vtools associate rare status -m "SKAT --name skat quantitative" --group_by refGene.name2 --to_db skat -j8
grybeate commented 4 years ago

I have run the commands. Everythings workes well before the last command and I get the following warnings:

INFO: Note: NumExpr detected 32 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
INFO: NumExpr defaulting to 8 threads.
INFO: 3180 samples are found
INFO: 2681 groups are found
Testing for association: 100% [==================================================================================================================================] 2,681/2,679 20.9/s in 00:02:08
refgene_name2   sample_size_skat        Q_stats_skat    pvalue_skat
WARNING: Field sample_size_skat has all missing values
WARNING: No valid integer values has been found for field sample_size_skat
WARNING: Field Q_stats_skat has all missing values
WARNING: No valid float values has been found for field Q_stats_skat
WARNING: Field pvalue_skat has all missing values
WARNING: No valid float values has been found for field pvalue_skat
INFO: Association tests on 2681 groups have completed. 2681 failed.
INFO: Using annotation DB skat as skat in project skat.
INFO: Annotation database used to record results of association tests. Created on Mon, 17 Feb 2020 12:04:23
INFO: 2681 out of 25360 refGene.refGene.name2 are annotated through annotation database skat
BoPeng commented 4 years ago

I cannot reproduce the problem after removing ~/.variant_tools/Rlib/SKAT. As you can see, SKAT 0.82.0 was automatically installed and could be used. 

INFO: Downloading SKAT (V0.82) ...
SKAT_0.82.tar.gz: 100% [======================================================================================] 701,582.0 2.4M/s in 00:00:00
INFO: Installing SKAT (V0.82) to /Users/bpeng1/.variant_tools/Rlib ...
INFO: 3180 samples are found
INFO: 2681 groups are found

Testing for association: 100% [================================================================================] 2,681/154 8.0/s in 00:05:33
INFO: Association tests on 2681 groups have completed. 154 failed.
INFO: Using annotation DB skat as skat in project skat.
INFO: Annotation database used to record results of association tests. Created on Tue, 18 Feb 2020 18:02:29
INFO: 2681 out of 25360 refGene.refGene.name2 are annotated through annotation database skat

@grybeate Could you also remove ~/.variant_tools/Rlib and re-download SKAT? Note that I have released vtools 3.1.2 for a bug that is probably related to this one.

grybeate commented 4 years ago

hi I will ask our bioinformatician to look into this on Monday. We have winter hollidays in Norway these days, so few people on work this week. Thanks again for looking into this, we will get back to you next week.

Best regards Gry

On Tue, Feb 18, 2020 at 7:11 PM Bo notifications@github.com wrote:

I cannot reproduce the problem after removing ~/.variant_tools/Rlib/SKAT. As you can see, SKAT 0.82.0 was automatically installed and could be used.

INFO: Downloading SKAT (V0.82) ... SKAT_0.82.tar.gz: 100% [======================================================================================] 701,582.0 2.4M/s in 00:00:00 INFO: Installing SKAT (V0.82) to /Users/bpeng1/.variant_tools/Rlib ... INFO: 3180 samples are found INFO: 2681 groups are found

Testing for association: 100% [================================================================================] 2,681/154 8.0/s in 00:05:33 INFO: Association tests on 2681 groups have completed. 154 failed. INFO: Using annotation DB skat as skat in project skat. INFO: Annotation database used to record results of association tests. Created on Tue, 18 Feb 2020 18:02:29 INFO: 2681 out of 25360 refGene.refGene.name2 are annotated through annotation database skat

@grybeate https://github.com/grybeate Could you also remove ~/.variant_tools/Rlib and re-download SKAT?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/vatlab/varianttools/issues/138?email_source=notifications&email_token=AMEEVKU7IK3AJXMXCTTS7NTRDQQFNA5CNFSM4KGY53J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMDAXMA#issuecomment-587598768, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMEEVKWXMOEMZCJMCWXXRYLRDQQFNANCNFSM4KGY53JQ .