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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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Yaml file don't work when using #617

Closed gulipeng17 closed 1 year ago

gulipeng17 commented 1 year ago

Hi ,Doctor: My comd is lirical-cli-2.0.0-RC2.jar yaml -y LDS2.yaml ，but the tools arise "ERROR o.m.l.c.c.AbstractPrioritizeCommand - Error: java.lang.NullPointerException: Cannot invoke "org.monarchinitiative.lirical.core.io.VariantParser.sampleNames()" because "variantParser" is null" My yaml file is the demo you provided :

          sampleId: Patient 4
          hpoIds: ['HP:0001659', 'HP:0001166', 'HP:0001631', 'HP:0000193', 'HP:0012385', 'HP:0011645', 'HP:0000272',
                   'HP:0000347', 'HP:0001655', 'HP:0000768', 'HP:0004927', 'HP:0002650', 'HP:0001704']
          # negatedHpoIds: []
          age: P9Y
          sex: FEMALE
          # Set real path to a VCF file
          vcf: LDS2.vcf.gz

What should I do next
ielis commented 1 year ago

Hi @gulipeng17 can you try the same command with the following YAML file?

## LIRICAL Analysis Template.
# These are all the possible options for running LIRICAL. Use this as a template for your own set-up.
---
sampleId: Patient 4
hpoIds: ['HP:0001659', 'HP:0001166', 'HP:0001631', 'HP:0000193', 'HP:0012385', 'HP:0011645', 'HP:0000272',
         'HP:0000347', 'HP:0001655', 'HP:0000768', 'HP:0004927', 'HP:0002650', 'HP:0001704']
# negatedHpoIds: []
age: P9Y
sex: FEMALE
# Set real path to a VCF file. For instance, path to the example `LDS2.vcf.gz` file located next to this YAML config.
# vcf: /path/to/LDS2.vcf.gz
gulipeng17 commented 1 year ago

Hi ,Doctor: I do as you say : First,using /path/to/LDS2.vcf.gz have the same issue； Sec, using # before /path/to/LDS2.vcf.gz file ,but has no gene result;

gulipeng17 commented 1 year ago

hi,@ielis Meet the above, how should I deal with?

ielis commented 1 year ago

It looks like you're trying to run LIRICAL with a VCF file using a YAML configuration file. For this to work, you must ensure the vcf field of the YAML file points to the VCF file. On top of that, you must provide the --assembly and -e19 (or -e38 depending on your build) options to the CLI. This was not explicitly stated in the docs before. However, the latest docs provide better instructions.

The complete command, should look like this if your VCF file uses hg38:

lirical yaml -y example.yml --assembly hg38 -e38 /path/to/exomiser/2302_hg38_variants.mv.db

Alternatively, run this for hg19:

lirical yaml -y example.yml --assembly hg19 -e19 /path/to/exomiser/2302_hg19_variants.mv.db
honglei28 commented 1 year ago

Hi @ielis

I am getting the same error even after providing the --assembly and -e19. Here is my command: lirical yaml -y examples/example.yaml --assembly hg19 -e19 $hg19_db -d $lirical_data

14:21:12.937 [main] ERROR o.m.l.c.c.AbstractPrioritizeCommand - Error: java.lang.NullPointerException: Cannot invoke "org.monarchinitiative.lirical.core.io.VariantParser.sampleNames()" because "variantParser" is null

I can get output without vcf input.

Below is the complete error message. it is weird that I am using hg19 genome build but the log is about hg38?

14:28:14.365 [main] INFO o.m.l.c.c.LiricalConfigurationCommand - Running LIRICAL from /AI/Bentchmark/LIRICAL_v2.0.0/lirical-cli-2.0.0-RC2/lirical-cli-2.0.0-RC2.jar 14:28:14.368 [main] INFO o.m.l.c.c.LiricalConfigurationCommand - Using data folder at /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data 14:28:19.344 [main] INFO o.m.l.c.c.AbstractPrioritizeCommand - Configured LIRICAL v2.0.0-RC2 14:28:19.344 [main] INFO o.m.l.c.c.AbstractPrioritizeCommand - Preparing the analysis data 14:28:19.361 [main] INFO o.m.lirical.cli.cmd.YamlCommand - Parsing YAML input file at examples/example.yaml 14:28:19.376 [main] INFO o.m.l.i.s.JannovarFunctionalVariantAnnotatorService - Loading transcript database from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/hg38_refseq.ser 14:28:19.376 [main] INFO d.c.c.j.data.JannovarDataSerializer - Deserializing JannovarData from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/hg38_refseq.ser 14:28:32.294 [main] INFO d.c.c.j.data.JannovarDataSerializer - Deserialization took 12.92 sec. 14:28:32.306 [main] WARN o.m.l.io.vcf.VcfVariantParserFactory - Cannot configure variant metadata service for HG38 14:28:32.307 [main] ERROR o.m.l.c.c.AbstractPrioritizeCommand - Error: java.lang.NullPointerException: Cannot invoke "org.monarchinitiative.lirical.core.io.VariantParser.sampleNames()" because "variantParser" is null

So I tried with hg38 sample and I can get proper result: lirical yaml -y examples/example_hg38.yaml --assembly hg38 -e38 $hg38_db -d $lirical_data

ielis commented 1 year ago

Hi @honglei28 can you please rerun the command with a -v option to increase verbosity of the reporting, and share the output?

Something like this:

lirical yaml -v -y examples/example.yaml --assembly hg19 -e19 $hg19_db  -d $lirical_data
honglei28 commented 1 year ago

Hi @ielis Here is the output with -v

LIkelihood Ratio Interpretation of Clinical AbnormaLities
                                    :: v2.0.0-RC2 ::

09:00:53.256 [main] INFO  o.m.l.c.c.LiricalConfigurationCommand - Running LIRICAL from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/lirical-cli/target/lirical-cli-2.0.0-RC2.jar
09:00:53.260 [main] INFO  o.m.l.c.c.LiricalConfigurationCommand - Using data folder at /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data
09:00:53.260 [main] DEBUG o.m.l.c.c.AbstractPrioritizeCommand - Using genome build HG19
09:00:53.261 [main] DEBUG o.m.l.c.c.AbstractPrioritizeCommand - Using RefSeq transcripts
09:00:53.264 [main] DEBUG o.m.lirical.configuration.LoadUtils - Loading HPO from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/hp.json
09:00:53.317 [main] DEBUG o.m.phenol.io.OntologyLoader - Read first bytes: {
  "graphs" : [
09:00:53.317 [main] DEBUG o.m.phenol.io.OntologyLoader - Looks like a JSON file...
09:00:53.817 [main] DEBUG o.m.phenol.io.OntologyLoader - Finished loading ontology
09:00:53.817 [main] DEBUG o.m.phenol.io.OntologyLoader - Creating phenol ontology
09:00:53.819 [main] DEBUG o.m.p.i.o.OboGraphDocumentAdaptor - Converting graph document...
09:00:53.819 [main] DEBUG o.m.p.i.o.OboGraphDocumentAdaptor - Converting metadata...
09:00:53.821 [main] DEBUG o.m.p.i.o.OboGraphDocumentAdaptor - Converting nodes to terms...
09:00:53.901 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_0045087 Hip joint hypermobility
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200100 Facial expressions not directed to others
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200101 Limited Repertoire of gestures
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200102 Reduced social smiling
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200103 Reduced social responsiveness
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200110 Preferes being alone
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200113 Offers information
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200116 Difficulty understanding nonliteral meaning of conversation
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200117 Poor recognition of injustice
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200118 Difficulty recognizing another's emotions
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200119 Difficulty understanding humor
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200120 Abnormality in emotional social interactions
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200121 Treats people like objects
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200122 Difficulty communicating ones emotions
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200123 Abnormal response to social norms
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200124 Indifference to social norms
09:00:53.908 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200128 Deficit applying language skills across context
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200130 Insistence on sameness
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200131 Reduced use of language for social purposes
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200132 Atypical sensory examination of objects
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200133 Intense attachment to unusual objects
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200135 Delay in the acquisition of play skills
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200136 Reduced social reciprocity with peers
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphTermFactory - No meta instance exists for node: http://purl.obolibrary.org/obo/HP_5200137 Reduced attempt to get or direct attention of peers
09:00:53.909 [main] DEBUG o.m.p.i.o.OboGraphDocumentAdaptor - Converting edges to relationships...
09:00:54.052 [main] DEBUG o.m.p.g.util.CompatibilityChecker - Checking vertices (17664) and edges (21975) for compatibility...
09:00:54.066 [main] DEBUG o.m.p.g.util.CompatibilityChecker - Vertices and edges are compatible!
09:00:54.075 [main] DEBUG o.m.p.g.util.CompatibilityChecker - Graph is simple!
09:00:54.219 [main] DEBUG o.m.phenol.io.OntologyLoader - Parsed a total of 17664 terms
09:00:54.219 [main] DEBUG o.m.lirical.configuration.LoadUtils - Loading HPO annotations from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/phenotype.hpoa
09:00:54.256 [main] DEBUG o.m.p.a.i.h.HpoaDiseaseDataLoaderDefault - Detected HPO annotations version 2023-10-09
09:00:54.256 [main] DEBUG o.m.p.a.i.h.HpoaDiseaseDataLoaderDefault - HPO version used to generate the annotations 2023-10-09
09:00:55.180 [main] DEBUG o.m.p.a.f.h.HpoAssociationDataBuilder - Gene identifiers are unset.
09:00:55.180 [main] DEBUG o.m.p.a.f.h.HpoAssociationDataBuilder - Loading gene identifiers from HGNC complete set archive file at /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/hgnc_complete_set.txt
09:00:55.190 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:372   AKAP2   A-kinase anchoring protein 2    other   complex locus constituent   Approved    9q31.3  09q31.3 "AKAP-KL|KIAA0920|DKFZp564L0716|MISP2"  protein kinase A2   PRKA2   A kinase (PRKA) anchor protein 2    A-kinase anchoring proteins 396 1999-09-16      2015-11-17  2023-01-20          OTTHUMG00000156811  uc004bem.4  AB023137    Q9Y2D5  10231032    MGI:1306795                                                                 '
09:00:55.197 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:40006 BACH1-IT1   BACH1 intronic transcript 1 non-coding RNA  RNA, long non-coding    Approved    21q21.3 21q21.3             BACH1 intronic transcript 1 (non-protein coding)    Intronic transcripts    1989    2011-04-28      2015-02-25  2015-02-25      ENSG00000248476 OTTHUMG00000078881  uc061zlk.1  AF317902        BACH1-IT1               '
09:00:55.209 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:55933 CHILL1  cancer hallmarks in lung lncRNA 1   non-coding RNA  RNA, long non-coding    Approved    8p21.3  08p21.3                 Long non-coding RNAs with non-systematic symbols    1992022-10-26       2022-11-08  2023-04-26      ENSG00000253616                         36778670                '
09:00:55.216 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:2613  CYP2A7P2    cytochrome P450 family 2 subfamily A member 7 pseudogene 2  pseudogene  pseudogene  Approved    19q13.2 19q13.2 CYP2A18PC           cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7, pseudogene 2           1995-12-13      2003-01-14  2017-03-23      ENSG00000198251 OTTHUMG00000182829  7668294                                         PGOHUM00000295008                               '
09:00:55.218 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:37107 DDX11L6 DEAD/H-box helicase 11 like 6 (pseudogene)  pseudogene  pseudogene  Approved    9q34.3  09q34.3             "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 6|DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 6|DEAD/H-box helicase 11 like 6"          2010-04-08      2020-02-17  2020-02-17                  19476624                                                                                    '
09:00:55.218 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:37108 DDX11L7 DEAD/H-box helicase 11 like 7 (pseudogene)  pseudogene  pseudogene  Approved    11p15.5 11p15.5             "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 7|DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 7|DEAD/H-box helicase 11 like 7"          2010-04-08      2020-02-17  2020-02-17                  19476624                                                                                    '
09:00:55.218 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:37112 DDX11L13    DEAD/H-box helicase 11 like 13 (pseudogene) pseudogene  pseudogene  Approved    20p13   20p13               "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 13|DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 13|DEAD/H-box helicase 11 like 13"           2010-04-08      2020-02-17  2020-02-17          19476624                                                                                    '
09:00:55.218 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:37114 DDX11L15    DEAD/H-box helicase 11 like 15 (pseudogene) pseudogene  pseudogene  Approved    Xp11.32 Xp11.32             "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 15|DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 15|DEAD/H-box helicase 11 like 15"           2010-04-08      2020-02-17  2020-02-17          19476624                                                                                    '
09:00:55.220 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:50449 DNAJB5P1    DnaJ heat shock protein family (Hsp40) member B5 pseudogene 1   pseudogene  pseudogene  Approved    9q21.2  09q21.2             DnaJ (Hsp40) homolog, subfamily B, member 5 pseudogene 1            2014-04-30      2015-11-19  2020-01-22      ENSG00000230335 OTTHUMG00000020048                  PGOHUM00000236217                                                               '
09:00:55.223 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:3142  EBVM1   Epstein Barr virus modification site 1  other   region  Approved    11q23.1 11q23.1                         2001-06-22          2020-01-30              "2843323|14526168|1327661"                                                                      '
09:00:55.227 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:53421 ERVH-8  endogenous retrovirus group H member 8, envelope    other   endogenous retrovirus   Approved    2q24.3  02q24.3 envH1               Envelope ERV derived genes  1412    2017-03-30      2017-03-30                  AJ289709                12970426                                    '
09:00:55.227 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:53422 ERVH-9  endogenous retrovirus group H member 9, envelope    other   endogenous retrovirus   Approved    3q26.1  03q26.1 envH2               Envelope ERV derived genes  1412    2017-03-30      2017-03-30                  AJ289710                "11162811|12970426"                             '
09:00:55.227 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:53423 ERVH-10 endogenous retrovirus group H member 10, envelope   other   endogenous retrovirus   Approved    2q24.1  02q24.1 "envH3|envH/p59"                Envelope ERV derived genes  1412    2017-03-30          2017-03-30                  AJ289711                "11162811|12970426"                 '
09:00:55.232 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:3897  FRA3B   fragile site, aphidicolin type, common, fra(3)(p14.2)   other   fragile site    Approved    3p14.2  03p14.2                         1986-01-01          2003-10-09  3864602                                                                                 '
09:00:55.239 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:51728 GTF2IP16    general transcription factor IIi pseudogene 16  pseudogene  pseudogene  Approved    1q43    01q43                           2015-05-18          2015-05-18                                                                              PGOHUM00000296137                                                               '
09:00:55.239 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:51733 GTF2IP21    general transcription factor IIi pseudogene 21  pseudogene  pseudogene  Approved    1p36.33 01p36.33                            2015-05-18          2015-05-18                                                                              PGOHUM00000295517                                                               '
09:00:55.264 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:56876 LNCPTCTS    lncRNA papillary thyroid carcinoma tumor suppressor non-coding RNA  RNA, long non-coding    Approved    16p13.3 16p13.3 RP11-616M22.2   lncRNA in Papillary Thyroid Carcinoma as Tumor Suppressor   Long non-coding RNAs with non-systematic symbols    1992    2023-09-25          2023-09-25      ENSG00000259910                     37741431                                                                                    '
09:00:55.276 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7409  MT-7SDNA    mitochondrially encoded 7S DNA  other   region  Approved    mitochondria    mitochondria            MT7SDNA 7S DNA  Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  "24709344|273237"                           '
09:00:55.276 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7416  MT-ATT  mitochondrially encoded membrane attachment site    other   region  Approved    mitochondria    mitochondria            MTATT   membrane attachment site    Mitochondrially encoded regions 1971989-10-11   2019-10-09  2005-02-15  2019-10-09                                                      '
09:00:55.276 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7424  MT-CSB1 mitochondrially encoded conserved sequence block I  other   region  Approved    mitochondria    mitochondria    CSB-I       MTCSB1  conserved sequence block I  Mitochondrially encoded regions 1971989-10-11   2019-10-09  2005-02-15  2019-10-09                                  2982153                 '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7425  MT-CSB2 mitochondrially encoded conserved sequence block II other   region  Approved    mitochondria    mitochondria    CSB-II      MTCSB2  conserved sequence block II Mitochondrially encoded regions 1971989-10-11   2019-10-09  2005-02-15  2019-10-09                                  2982153                 '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7426  MT-CSB3 mitochondrially encoded conserved sequence block III    other   region  Approved    mitochondria    mitochondria    CSB-III     MTCSB3  conserved sequence block III    Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  2982153         '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7438  MT-HPR  mitochondrially encoded replication primer  other   region  Approved    mitochondria    mitochondria    HPR     MTHPR   replication primer  Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  3582365                         '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7439  MT-HSP1 mitochondrially encoded major H-strand promoter other   region  Approved    mitochondria    mitochondria            MTHSP1  major H-strand promoter Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  6185947                     '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7440  MT-HSP2 mitochondrially encoded minor H-strand promoter other   region  Approved    mitochondria    mitochondria            MTHSP2  minor H-strand promoter Mitochondrially encoded regions 1973    1989-10-12  2019-10-09  2005-02-15  2019-10-09                                  6185947                     '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:50279 MT-LIPCAR   mitochondrially encoded long non-coding cardiac associated RNA  non-coding RNA  RNA, long non-coding    Approved    mitochondria    mitochondria    "uc022bqs.1|LIPCAR" long intergenic non coding RNA predicting cardiac remodeling and survival           "Mitochondrially encoded long non-coding RNAs|Long non-coding RNAs with non-systematic symbols" "1976|1992" 2014-06-27      2014-06-27  2020-01-22                  JA760602                24663402    mt-lipcar                               '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7447  MT-LSP  mitochondrially encoded L-strand promoter   other   region  Approved    mitochondria    mitochondria            MTLSP   L-strand promoter   Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  6185947                         '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7465  MT-OHR  mitochondrially encoded heavy strand origin of replication  other   region  Approved    mitochondria    mitochondria            MTOHR   heavy strand origin of replication  Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  551247      '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7466  MT-OLR  mitochondrially encoded light strand origin of replication  other   region  Approved    mitochondria    mitochondria    OriL        MTOLR   light strand origin of replication  Mitochondrially encoded regions 1973    1989-10-12  2019-10-09  2005-02-15  2019-10-09                                  3944140     '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7472  MT-RNR3 mitochondrially encoded 5S-like sequence    other   region  Approved    mitochondria    mitochondria            MTRNR3  5S-like sequence    Mitochondrially encoded regions 1973    1989-10-12  2019-10-09  2005-02-15  2019-10-09                                  6180301                         '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7476  MT-TAS  mitochondrially encoded termination associated sequence other   region  Approved    mitochondria    mitochondria            MTTAS   "termination associated sequence|mitochondrially encoded termination associate sequence"    Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2019-10-09  2019-10-09                  9473475                                                                                 '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7480  MT-TER  mitochondrially encoded transcription terminator    other   region  Approved    mitochondria    mitochondria            MTTER   transcription terminator    Mitochondrially encoded regions 1971989-10-12   2019-10-09  2005-02-15  2019-10-09                                  3018722                 '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7482  MT-TFH  mitochondrially encoded transcription factor binding site H other   region  Approved    mitochondria    mitochondria            MTTFH   mitochondrial transcription factor binding site Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  3594571                                                                                 '
09:00:55.277 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7483  MT-TFL  mitochondrially encoded transcription factor binding site L other   region  Approved    mitochondria    mitochondria            MTTFL   mitochondrial transcription factor binding site Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  3594571                                                                                 '
09:00:55.278 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7484  MT-TFX  mitochondrially encoded transcription factor binding site X other   region  Approved    mitochondria    mitochondria            MTTFX   mitochondrial transcription factor binding site Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  3594571                                                                                 '
09:00:55.278 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:7485  MT-TFY  mitochondrially encoded transcription factor binding site Y other   region  Approved    mitochondria    mitochondria            MTTFY   mitochondrial transcription factor binding site Mitochondrially encoded regions 1973    1989-10-11  2019-10-09  2005-02-15  2019-10-09                                  3594571                                                                                 '
09:00:55.279 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:52320 MTND4P38    MT-ND4 pseudogene 38    pseudogene  pseudogene  Approved    15q21.3 15q21.3             mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 pseudogene 38     2016-07-22      2018-05-30  2018-05-30                                                          PGOHUM00000293252                                                               '
09:00:55.279 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:52327 MTND6P36    MT-ND6 pseudogene 36    pseudogene  pseudogene  Approved    7p11.2  07p11.2             mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 pseudogene 36     2016-07-22      2018-05-30  2018-05-30                                                          PGOHUM00000302197                                                               '
09:00:55.286 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:15845 PALM2   paralemmin 2    other   complex locus constituent   Approved    9q31.3  09q31.3                 Paralemmins 1792    2001-08-30          2023-01-20          OTTHUMG00000020479  uc004beg.4  AJ312216            Q8IXS6  11478809                                            '
09:00:55.317 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:54925 SLC7A2-IT1  SLC7A2 intronic transcript 1    non-coding RNA  RNA, long non-coding    Approved    8p22    08p22                   Intronic transcripts    1989    2020-04-29          2020-04-29      ENSG00000279903         AV720089                22411793                                '
09:00:55.362 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:54208 TRA-AGC13-3 tRNA-Ala (anticodon AGC) 13-3   non-coding RNA  RNA, transfer   Approved    6p22.2  06p22.2 tRNA-Ala-AGC-13-3                       2019-04-03          2019-04-03                                                                                  '
09:00:55.364 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:54204 TRE-TTC8-2  tRNA-Glu (TTC) 8-2  non-coding RNA  RNA, transfer   Approved    1p22.1  01p22.1 tRNA-Glu-TTC-8-2                Low confidence cytoplasmic transfer RNAs    1877    2019-03-28          2019-03-28                                                                  '
09:00:55.366 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:52409 TRMT10BP1   tRNA methyltransferase 10B pseudogene 1 pseudogene  pseudogene  Approved    8q23.1  08q23.1                         2016-11-01          2020-01-22  ENSG00000253580 OTTHUMG00000164882                                                                  PGOHUM00000303657                                                               '
09:00:55.367 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:54203 TRN-GTT15-2 tRNA-Asn (GTT) 15-2 non-coding RNA  RNA, transfer   Approved    1q21.1  01q21.1 tRNA-Asn-GTT-15-2               Low confidence cytoplasmic transfer RNAs    1877    2019-03-28          2019-03-28                                                                  '
09:00:55.367 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:54205 TRN-GTT19-2 tRNA-Asn (GTT) 19-2 non-coding RNA  RNA, transfer   Approved    1p11.2  01p11.2 tRNA-Asn-GTT-19-2               Low confidence cytoplasmic transfer RNAs    1877    2019-03-28          2019-03-28                                                                  '
09:00:55.367 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:54206 TRQ-CTG8-3  tRNA-Gln (CTG) 8-3  non-coding RNA  RNA, transfer   Approved    21p11.2 21p11.2 tRNA-Gln-CTG-8-3                Low confidence cytoplasmic transfer RNAs    1877    2019-03-28          2019-03-28                                                                  '
09:00:55.368 [main] DEBUG o.m.p.a.a.HGNCGeneIdentifierLoader - Skipping line with missing Entrez ID 'HGNC:35096 TRR-CCT6-1  tRNA-Arg (anticodon CCT) 6-1    pseudogene  pseudogene  Approved    1q21.1  01q21.1 tRNA-Arg-CCT-6-1        TRNAR33P    "transfer RNA arginine 33 (anticodon CCU) pseudogene|transfer RNA-Arg (CCT) 6-1"    Cytoplasmic transfer RNA pseudogenes    1681    2008-08-29  2014-06-19  2019-05-01  2019-05-01                  HG983610                                                                                    tRNA-Arg-CCT-6-1            '
09:00:55.384 [main] DEBUG o.m.p.a.f.h.HpoAssociationDataBuilder - Disease to gene associations are unset.
09:00:55.384 [main] DEBUG o.m.p.a.f.h.HpoAssociationDataBuilder - Loading disease to gene associations from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/mim2gene_medgen
09:00:55.460 [main] DEBUG o.m.p.a.f.h.HpoAssociationDataBuilder - HPO gene annotations are unset.
09:00:55.460 [main] DEBUG o.m.p.a.f.h.HpoAssociationDataBuilder - Loading HPO gene annotations.
09:00:55.769 [main] DEBUG o.m.l.configuration.LiricalBuilder - Using bundled variant background frequencies
09:00:55.770 [main] DEBUG o.m.l.configuration.LiricalBuilder - Functional variant annotator service is unset. Creating the service using resources in /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data.
09:00:55.774 [main] DEBUG o.m.l.i.s.JannovarFunctionalVariantAnnotatorService - Configured Jannovar functional annotators for HG38 -> RefSeq, HG38 -> ucsc, HG19 -> RefSeq, HG19 -> ucsc
09:00:55.774 [main] DEBUG o.m.l.configuration.LiricalBuilder - Variant metadata service is unset.
09:00:55.774 [main] DEBUG o.m.l.configuration.LiricalBuilder - Using Exomiser variant databases: {HG19 -> /AI/Bentchmark/LIRICAL_v2.0.0/2302_hg19/2302_hg19_variants.mv.db}
09:00:58.774 [main] DEBUG o.m.l.c.a.i.LiricalAnalysisRunnerImpl - Creating LIRICAL pool with 40 workers.
09:00:58.776 [main] INFO  o.m.l.c.c.AbstractPrioritizeCommand - Configured LIRICAL v2.0.0-RC2
09:00:58.776 [main] INFO  o.m.l.c.c.AbstractPrioritizeCommand - Preparing the analysis data
09:00:58.797 [main] INFO  o.m.lirical.cli.cmd.YamlCommand - Parsing YAML input file at lirical-cli-2.0.0-RC2/examples/example.yaml
09:00:58.806 [main] DEBUG o.m.l.i.a.BaseAnalysisDataParser - The age was not provided
09:00:58.809 [main] DEBUG o.m.l.i.s.JannovarFunctionalVariantAnnotatorService - Loading transcript database for HG38:RefSeq
09:00:58.810 [main] INFO  o.m.l.i.s.JannovarFunctionalVariantAnnotatorService - Loading transcript database from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/hg38_refseq.ser
09:00:58.811 [main] INFO  d.c.c.j.data.JannovarDataSerializer - Deserializing JannovarData from /AI/Bentchmark/LIRICAL_v2.0.0/LIRICAL/data/hg38_refseq.ser
09:01:11.237 [main] INFO  d.c.c.j.data.JannovarDataSerializer - Deserialization took 12.43 sec.
09:01:11.250 [main] WARN  o.m.l.io.vcf.VcfVariantParserFactory - Cannot configure variant metadata service for HG38
09:01:11.250 [main] ERROR o.m.l.c.c.AbstractPrioritizeCommand - Error: java.lang.NullPointerException: Cannot invoke "org.monarchinitiative.lirical.core.io.VariantParser.sampleNames()" because "variantParser" is null
09:01:11.250 [main] DEBUG o.m.l.c.c.AbstractPrioritizeCommand - More info:
org.monarchinitiative.lirical.core.analysis.LiricalParseException: java.lang.NullPointerException: Cannot invoke "org.monarchinitiative.lirical.core.io.VariantParser.sampleNames()" because "variantParser" is null
    at org.monarchinitiative.lirical.io.analysis.BaseAnalysisDataParser.parseGeneToGenotype(BaseAnalysisDataParser.java:72)
    at org.monarchinitiative.lirical.io.analysis.YamlAnalysisDataParser.parse(YamlAnalysisDataParser.java:54)
    at org.monarchinitiative.lirical.cli.cmd.YamlCommand.prepareAnalysisData(YamlCommand.java:51)
    at org.monarchinitiative.lirical.cli.cmd.AnalysisDataParserAwareCommand.prepareAnalysisData(AnalysisDataParserAwareCommand.java:17)
    at org.monarchinitiative.lirical.cli.cmd.AbstractPrioritizeCommand.execute(AbstractPrioritizeCommand.java:98)
    at org.monarchinitiative.lirical.cli.cmd.YamlCommand.execute(YamlCommand.java:22)
    at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:31)
    at org.monarchinitiative.lirical.cli.cmd.YamlCommand.call(YamlCommand.java:22)
    at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:18)
    at picocli.CommandLine.executeUserObject(CommandLine.java:2041)
    at picocli.CommandLine.access$1500(CommandLine.java:148)
    at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2453)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2415)
    at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273)
    at picocli.CommandLine$RunLast.execute(CommandLine.java:2417)
    at picocli.CommandLine.execute(CommandLine.java:2170)
    at org.monarchinitiative.lirical.cli.Main.main(Main.java:43)
Caused by: java.lang.NullPointerException: Cannot invoke "org.monarchinitiative.lirical.core.io.VariantParser.sampleNames()" because "variantParser" is null
    at org.monarchinitiative.lirical.io.analysis.BaseAnalysisDataParser.parseGeneToGenotype(BaseAnalysisDataParser.java:43)
    ... 17 common frames omitted
ielis commented 1 year ago

Hi @honglei28 sorry, this is a true bug in the RC2 code, where a default genome build (hg38) is used instead of the build provided via --assembly CLI option (hg19 in your case). The bug has already been fixed in 30dbcffd but the fix has not yet made it into the latest release.

So, there are two options to move forward:

Thanks for letting us know about the bug and all the best, Daniel

honglei28 commented 1 year ago

lirical prioritize works. Thanks for your prompt response!