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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
49 stars 25 forks source link

tests failing #70

Open rachelss opened 8 years ago

rachelss commented 8 years ago

On Mac

env CTEST_OUTPUT_ON_FAILURE=1 make test

Verbose output:

Running tests...
Test project /Users/rachelschwartz/Desktop/ASU/denovogear/build
      Start  1: test_bcf_build
 1/22 Test  #1: test_bcf_build ...................***Failed    0.13 sec
Linking CXX executable test_bcf
Undefined symbols for architecture x86_64:
  "_main", referenced from:
     implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[4]: *** [test/test_bcf] Error 1
make[3]: *** [test/CMakeFiles/test_bcf.dir/all] Error 2
make[2]: *** [test/CMakeFiles/test_bcf.dir/rule] Error 2
make[1]: *** [test_bcf] Error 2

      Start  2: test_bcf_run
Could not find executable test_bcf
Looked in the following places:
test_bcf
test_bcf
Release/test_bcf
Release/test_bcf
Debug/test_bcf
Debug/test_bcf
MinSizeRel/test_bcf
MinSizeRel/test_bcf
RelWithDebInfo/test_bcf
RelWithDebInfo/test_bcf
Deployment/test_bcf
Deployment/test_bcf
Development/test_bcf
Development/test_bcf
 2/22 Test  #2: test_bcf_run .....................***Not Run   0.00 sec
      Start  3: test_extra_build
 3/22 Test  #3: test_extra_build .................***Failed    0.12 sec
Linking CXX executable test_extra
Undefined symbols for architecture x86_64:
  "_main", referenced from:
     implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[4]: *** [test/test_extra] Error 1
make[3]: *** [test/CMakeFiles/test_extra.dir/all] Error 2
make[2]: *** [test/CMakeFiles/test_extra.dir/rule] Error 2
make[1]: *** [test_extra] Error 2

      Start  4: test_extra_run
Could not find executable test_extra
Looked in the following places:
test_extra
test_extra
Release/test_extra
Release/test_extra
Debug/test_extra
Debug/test_extra
MinSizeRel/test_extra
MinSizeRel/test_extra
RelWithDebInfo/test_extra
RelWithDebInfo/test_extra
Deployment/test_extra
Deployment/test_extra
Development/test_extra
Development/test_extra
 4/22 Test  #4: test_extra_run ...................***Not Run   0.00 sec
      Start  5: test_seq_build
 5/22 Test  #5: test_seq_build ...................***Failed    0.13 sec
Linking CXX executable test_seq
Undefined symbols for architecture x86_64:
  "_main", referenced from:
     implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[4]: *** [test/test_seq] Error 1
make[3]: *** [test/CMakeFiles/test_seq.dir/all] Error 2
make[2]: *** [test/CMakeFiles/test_seq.dir/rule] Error 2
make[1]: *** [test_seq] Error 2

      Start  6: test_seq_run
Could not find executable test_seq
Looked in the following places:
test_seq
test_seq
Release/test_seq
Release/test_seq
Debug/test_seq
Debug/test_seq
MinSizeRel/test_seq
MinSizeRel/test_seq
RelWithDebInfo/test_seq
RelWithDebInfo/test_seq
Deployment/test_seq
Deployment/test_seq
Development/test_seq
Development/test_seq
 6/22 Test  #6: test_seq_run .....................***Not Run   0.00 sec
      Start  7: test_utilities_build
 7/22 Test  #7: test_utilities_build .............***Failed    0.20 sec
Linking CXX executable test_utilities
Undefined symbols for architecture x86_64:
  "_main", referenced from:
     implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[4]: *** [test/test_utilities] Error 1
make[3]: *** [test/CMakeFiles/test_utilities.dir/all] Error 2
make[2]: *** [test/CMakeFiles/test_utilities.dir/rule] Error 2
make[1]: *** [test_utilities] Error 2

      Start  8: test_utilities_run
Could not find executable test_utilities
Looked in the following places:
test_utilities
test_utilities
Release/test_utilities
Release/test_utilities
Debug/test_utilities
Debug/test_utilities
MinSizeRel/test_utilities
MinSizeRel/test_utilities
RelWithDebInfo/test_utilities
RelWithDebInfo/test_utilities
Deployment/test_utilities
Deployment/test_utilities
Development/test_utilities
Development/test_utilities
 8/22 Test  #8: test_utilities_run ...............***Not Run   0.00 sec
      Start  9: CALL_Help
 9/22 Test  #9: CALL_Help ........................   Passed    0.01 sec
      Start 10: CALL_Sample5.3_BAM
10/22 Test #10: CALL_Sample5.3_BAM ...............   Passed    1.10 sec
      Start 11: CALL_Sample5.3_VCF
11/22 Test #11: CALL_Sample5.3_VCF ...............***Failed  Required regular expression not found.Regex=[76,1,0
]  0.01 sec
[vcf.c:1166 bcf_write] Broken VCF record, the number of columns at 5:126385924 does not match the number of samples (0 vs 5).
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##DeNovoGearCommandLine=<ID=dng-call,Version=1.1.1-94-gfdf6a63-dirty,Date="2015-10-30T14:55:57-0700",Epoch=1446242157531,CommandLineOptions="--fasta='' --gamma=0.98,0.0005,0.0005,1.04 --gamma=0.02,0.075,0.005,1.18 --min-qlen=0 --min-prob=0.001 --mu=1.0e-08 --mu-somatic=1.0e-08 --mu-library=1.0e-08 --nuc-freqs='0.3,0.2,0.2,0.3' --ped='/Users/rachelschwartz/Desktop/ASU/denovogear/testdata/sample_5_3/ceu.ped' --min-basequal=13 --min-mapqual=0 --region='' --ref-weight=1.0 --sam-files='' --theta=0.001 --output='-' --rgtag='LB' /Users/rachelschwartz/Desktop/ASU/denovogear/testdata/sample_5_3/test1.vcf">
##INFO=<ID=MUP,Number=1,Type=Float,Description="Probability of at least 1 de novo mutation">
##INFO=<ID=MU1P,Number=1,Type=Float,Description="Probability of exactly 1 de novo mutation">
##INFO=<ID=MUX,Number=1,Type=Float,Description="Expected number of de novo mutations">
##INFO=<ID=LLD,Number=1,Type=Float,Description="Log10-likelihood of observed data at the site">
##INFO=<ID=LLH,Number=1,Type=Float,Description="Scaled log10-likelihood of data at the site">
##INFO=<ID=DNT,Number=1,Type=String,Description="De novo type">
##INFO=<ID=DNL,Number=1,Type=String,Description="De novo location">
##INFO=<ID=DNQ,Number=1,Type=Integer,Description="Phread-scaled de novo quality">
##INFO=<ID=DNC,Number=1,Type=Integer,Description="De novo location certainty">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth">
##INFO=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##INFO=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed (forward strand)">
##INFO=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed (reverse strand)">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=MQTa,Number=1,Type=Float,Description="Anderson-Darling Ta statistic for Alt vs. Ref read mapping qualities">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Phred-scaled genotype quality">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype posterior probabilities">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-likelihood of genotype based on read depths">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed (forward strand)">
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed (reverse strand)">
##FORMAT=<ID=MUP,Number=1,Type=Float,Description="Probability of at least 1 de novo mutation in this node.">
##FORMAT=<ID=MU1P,Number=1,Type=Float,Description="Conditional probability that this node contains a de novo mutation given only 1 de novo mutation">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##META=<ID=FatherMR,Type=Float,Number=1,Description="Paternal mutation rate parameter">
##META=<ID=MotherMR,Type=Float,Number=1,Description="Maternal mutation rate parameter">
##META=<ID=OriginalMR,Type=Float,Number=1,Description="Somatic or library mutation rate parameter">
##PEDIGREE=<ID=LB-NA12878:Solexa-135852,Father=GL-1,Mother=GL-2,FatherMR=3.0e-08,MotherMR=3.0e-08>
##PEDIGREE=<ID=LB-NA12891:Solexa-135851,Original=GL-1,OriginalMR=2.0e-08>
##PEDIGREE=<ID=LB-NA12892:Solexa-135853,Original=GL-2,OriginalMR=2.0e-08>
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  GL-1    GL-2    LB-NA12878:Solexa-135852    LB-NA12891:Solexa-135851    LB-NA12892:Solexa-135853

      Start 12: DNM_Help
12/22 Test #12: DNM_Help .........................   Passed    0.01 sec
      Start 13: DNM_InputErr
13/22 Test #13: DNM_InputErr .....................   Passed    0.00 sec
      Start 14: DNM_SampleCEU
14/22 Test #14: DNM_SampleCEU ....................   Passed    0.01 sec
      Start 15: DNM_SamplePaired
15/22 Test #15: DNM_SamplePaired .................   Passed    0.01 sec
      Start 16: DNM_ATMutation
16/22 Test #16: DNM_ATMutation ...................***Failed  Required regular expression not found.Regex=[flag: 0
]  0.01 sec

Created SNP lookup table
 First mrate: 1 last: 0
 First code: 9 last: 1
 First target string: AA/AA/AA last: TT/TT/TT
 First tref: 9.66184e-09 last: 2

Created indel lookup table First code: 9 last: 0
 First target string: RR/RR/RR last: DD/DD/DD
 First prior: 0.228 last: 2

Created paired lookup table
 First target string: AA/AA last: TT/TT
 First prior 1 last: 1

Unable to open PED file, Exiting !

      Start 17: Phaser_Help
17/22 Test #17: Phaser_Help ......................   Passed    0.00 sec
      Start 18: Phaser_InputErr
18/22 Test #18: Phaser_InputErr ..................   Passed    0.00 sec
      Start 19: Phaser_Sample
19/22 Test #19: Phaser_Sample ....................   Passed    0.00 sec
      Start 20: CALL_Sample5.3_BAM_LB_TAG
20/22 Test #20: CALL_Sample5.3_BAM_LB_TAG ........   Passed    1.09 sec
      Start 21: CALL_Sample5.3_BAM_SM_TAG
21/22 Test #21: CALL_Sample5.3_BAM_SM_TAG ........   Passed    1.10 sec
      Start 22: CALL_Sample5.3_BAM_ID_TAG
22/22 Test #22: CALL_Sample5.3_BAM_ID_TAG ........   Passed    1.09 sec

55% tests passed, 10 tests failed out of 22

Total Test time (real) =   5.03 sec

The following tests FAILED:
      1 - test_bcf_build (Failed)
      2 - test_bcf_run (Not Run)
      3 - test_extra_build (Failed)
      4 - test_extra_run (Not Run)
      5 - test_seq_build (Failed)
      6 - test_seq_run (Not Run)
      7 - test_utilities_build (Failed)
      8 - test_utilities_run (Not Run)
     11 - CALL_Sample5.3_VCF (Failed)
     16 - DNM_ATMutation (Failed)
reedacartwright commented 8 years ago

@kaeldai What do you think?

kaeldai commented 8 years ago

It is an issue with boost unit tests. Some combinations of clang/boost don't automatically add a main() to the unit tests, and we need to explicitly define BOOST_TEST_DYN_LINK macro. I was able to reproduce the issue on a linux machine, and have a fix here. I may need to add some extra compilation options to get it to fully work with OSX, but I don't have access to a mac at the moment so I'm holding off pushing to develop.

Also added some tests and found the test/CMakeLists was pulling from the wrong testdata directory.

kaeldai commented 8 years ago

@rachelss, when you have time can you pull a new dng-branch from https://github.com/kaeldai/denovogear/tree/hotfix/issue70 and run "make test" again? Thanks.

stevenhwu commented 8 years ago

low priority by default github link "Test #[0-9]+", "Test #70" in the comment to issues and PR. One way to hack around it is put into code. e.g. #100 Are these any other hack we can use?

dwinter commented 8 years ago

@stevenhwu Apparently and kind of styling. So

But these come from the output of tests right? We could use a template (#103) that asks uses to place all the output in one big code block:

17/22 Test #17: Phaser_Help ...................... Passed 0.00 sec
Start 18: Phaser_InputErr
18/22 Test #18: Phaser_InputErr .................. Passed 0.00 sec
Start 19: Phaser_Sample
19/22 Test #19: Phaser_Sample .................... Passed 0.00 sec
Start 20: CALL_Sample5.3_BAM_LB_TAG
20/22 Test #20: CALL_Sample5.3_BAM_LB_TAG ........ Passed 1.09 sec
Start 21: CALL_Sample5.3_BAM_SM_TAG
21/22 Test #21: CALL_Sample5.3_BAM_SM_TAG ........ Passed 1.10 sec
Start 22: CALL_Sample5.3_BAM_ID_TAG
22/22 Test #22: CALL_Sample5.3_BAM_ID_TAG ........ Passed 1.09 sec

55% tests passed, 10 tests failed out of 22
reedacartwright commented 8 years ago

Update the OP to use code blocks

stevenhwu commented 8 years ago

Is this one ready to close?