I am attempting to add MISTIC functional prediction to a VCF using Funcotator. I have constructed a TSV file as follows (in the appropriate directory structure):

Chr     Start   End     ALT_BASES       MISTIC_SCORES   MISTIC_Predictions

chr1    150991026       150991026       G|A|    0.032969626362195414|0.032942329911215804|      B|B|

chr1    145752445       145752445       T|G|C|  0.5307351291992782|0.5575423227259573|0.5307351291992782|       D|D|D|

chr1    1431078 1431078 T|G|A|  0.16291235223539433|0.3462216660107844|0.4434115143402344|      B|B|B|

The "mistic.config" file follows:

name = mistic

version = 1

src_file = mistic_GRCh37.tsv

origin_location = MISTIC

preprocessing_script =

 

# Whether this data source is for the b37 reference.

# Required and defaults to false.

isB37DataSource = true

 

# Supported types:

# simpleXSV    -- Arbitrary separated value table (e.g. CSV), keyed off Gene Name OR Transcript ID

# locatableXSV -- Arbitrary separated value table (e.g. CSV), keyed off a genome location

# gencode      -- Custom datasource class for GENCODE

#       cosmic       -- Custom datasource class for COSMIC

# vcf          -- Custom datasource class for Variant Call Format (VCF) files

type = locatableXSV

 

# Required field for GENCODE files.

# Path to the FASTA file from which to load the sequences for GENCODE transcripts:

gencode_fasta_path =

 

# Required field for GENCODE files.

# NCBI build version (either hg19 or hg38):

ncbi_build_version = 

 

# Required field for simpleXSV files.

# Valid values:

#     GENE_NAME

#     TRANSCRIPT_ID

xsv_key =

 

# Required field for simpleXSV files.

# The 0-based index of the column containing the key on which to match

xsv_key_column = 

 

# Required field for simpleXSV AND locatableXSV files.

# The delimiter by which to split the XSV file into columns.

xsv_delimiter = \t

 

# Required field for simpleXSV files.

# Whether to permissively match the number of columns in the header and data rows

# Valid values:

#     true

#     false

xsv_permissive_cols =

 

# Required field for locatableXSV files.

# The 0-based index of the column containing the contig for each row

contig_column = 0

 

# Required field for locatableXSV files.

# The 0-based index of the column containing the start position for each row

start_column = 1

 

# Required field for locatableXSV files.

# The 0-based index of the column containing the end position for each row

end_column = 2

 

 

 

I am using GATK version 4.2.6.1

 

 

b) Exact command used:

$ java -Xmx1024m -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar $LIBPATH/gatk-package-4.2.6.1-local.jar Funcotator \

>     --data-sources-path ${ANNOTATIONS} \

>     --variant ${TMP}/${f}.LyCEUM.mutect2.filtered.vcf \

>     --output ${OUTPATH}/${f}.LyCEUM.SNV.vcf \

>     --reference ${HGREF} \

>     --ref-version hg19 \

>     --output-file-format VCF \

>     --remove-filtered-variants false \

>     --tmp-dir ${TMP} \

>     --transcript-selection-mode BEST_EFFECT

c) Entire program log:

 

01:21:16.095 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/base/lyceum/rlib/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so

01:21:16.454 INFO  Funcotator - ------------------------------------------------------------

01:21:16.454 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.2.6.1

01:21:16.454 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/

01:21:16.454 INFO  Funcotator - Executing as base@basement-b on Linux v4.15.0-188-generic amd64

01:21:16.455 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v11.0.15+10-Ubuntu-0ubuntu0.18.04.1

01:21:16.455 INFO  Funcotator - Start Date/Time: July 4, 2022 at 1:21:16 AM UTC

01:21:16.455 INFO  Funcotator - ------------------------------------------------------------

01:21:16.455 INFO  Funcotator - ------------------------------------------------------------

01:21:16.456 INFO  Funcotator - HTSJDK Version: 2.24.1

01:21:16.456 INFO  Funcotator - Picard Version: 2.27.1

01:21:16.456 INFO  Funcotator - Built for Spark Version: 2.4.5

01:21:16.456 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2

01:21:16.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

01:21:16.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

01:21:16.456 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

01:21:16.457 INFO  Funcotator - Deflater: IntelDeflater

01:21:16.457 INFO  Funcotator - Inflater: IntelInflater

01:21:16.457 INFO  Funcotator - GCS max retries/reopens: 20

01:21:16.457 INFO  Funcotator - Requester pays: disabled

01:21:16.457 INFO  Funcotator - Initializing engine

01:21:16.732 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/data/LyCEUM/analysis/lyceum_pipe/.tmp/MP_22_0027.LyCEUM.mutect2.filtered.vcf

01:21:16.766 INFO  Funcotator - Done initializing engine

01:21:16.766 INFO  Funcotator - Validating sequence dictionaries...

01:21:16.768 INFO  Funcotator - Processing user transcripts/defaults/overrides...

01:21:16.768 INFO  Funcotator - Initializing data sources...

01:21:16.770 INFO  DataSourceUtils - Initializing data sources from directory: /home/data/references/funcotator_dataSources_LyCEUM

01:21:16.770 WARN  DataSourceUtils - Could not read MANIFEST.txt: unable to log data sources version information.

01:21:16.786 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode.v34lift37.annotation.REORDERED.gtf -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf

01:21:16.786 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode.v34lift37.pc_transcripts.fa -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode/hg19/gencode.v34lift37.pc_transcripts.fa

01:21:16.791 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/CosmicCodingMuts.normal.vcf -> file:///home/data/references/funcotator_dataSources_LyCEUM/cosmic/hg19/CosmicCodingMuts.normal.vcf

01:21:16.796 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/hgnc_download_Nov302017.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/hgnc/hg19/hgnc_download_Nov302017.tsv

01:21:16.800 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/data/references/funcotator_dataSources_LyCEUM/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt

01:21:16.804 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/clinvar_20180401.vcf -> file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar/hg19/clinvar_20180401.vcf

01:21:16.807 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv

01:21:16.811 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode_xrefseq_v75_37.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv

01:21:17.594 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv

01:21:17.598 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/clinvar_hgmd.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar_hgmd/hg19/clinvar_hgmd.tsv

01:21:17.602 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/hg19_All_20180423.vcf.gz -> file:///home/data/references/funcotator_dataSources_LyCEUM/dbsnp/hg19/hg19_All_20180423.vcf.gz

01:21:17.602 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...

01:21:17.602 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode.v34lift37.annotation.REORDERED.gtf -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf

01:21:17.602 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000

01:21:17.700 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf

01:21:17.738 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode.v34lift37.pc_transcripts.fa -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode/hg19/gencode.v34lift37.pc_transcripts.fa

01:21:21.378 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/CosmicCodingMuts.normal.vcf -> file:///home/data/references/funcotator_dataSources_LyCEUM/cosmic/hg19/CosmicCodingMuts.normal.vcf

01:21:21.378 INFO  DataSourceUtils - Setting lookahead cache for data source: cosmic : 100000

01:21:21.826 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/cosmic/hg19/CosmicCodingMuts.normal.vcf

01:21:21.931 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/CosmicCodingMuts.normal.vcf -> file:///home/data/references/funcotator_dataSources_LyCEUM/cosmic/hg19/CosmicCodingMuts.normal.vcf

01:21:22.087 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/cosmic/hg19/CosmicCodingMuts.normal.vcf

01:21:22.216 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/hgnc_download_Nov302017.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/hgnc/hg19/hgnc_download_Nov302017.tsv

01:21:22.386 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/data/references/funcotator_dataSources_LyCEUM/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt

01:21:22.390 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/clinvar_20180401.vcf -> file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar/hg19/clinvar_20180401.vcf

01:21:22.390 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000

01:21:22.489 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar/hg19/clinvar_20180401.vcf

01:21:22.607 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/clinvar_20180401.vcf -> file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar/hg19/clinvar_20180401.vcf

01:21:22.813 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar/hg19/clinvar_20180401.vcf

01:21:22.925 INFO  DataSourceUtils - Setting lookahead cache for data source: mistic : 100000

01:21:23.030 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv

01:21:23.031 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic.config

01:21:23.034 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv

01:21:23.035 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.tsv

WARNING 2022-07-04 01:21:23 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

01:21:23.038 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode_xrefseq_v75_37.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv

01:21:23.253 INFO  DataSourceUtils - Setting lookahead cache for data source: gnomAD_genome : 100000

01:21:26.452 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.genomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz

01:21:41.834 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.genomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz

01:21:43.160 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv

01:21:43.994 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000

01:21:44.425 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/clinvar_hgmd.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar_hgmd/hg19/clinvar_hgmd.tsv

01:21:44.426 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar_hgmd/hg19/clinvar_hgmd.config

01:21:44.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/clinvar_hgmd.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar_hgmd/hg19/clinvar_hgmd.tsv

01:21:44.462 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/clinvar_hgmd.tsv -> file:///home/data/references/funcotator_dataSources_LyCEUM/clinvar_hgmd/hg19/clinvar_hgmd.tsv

WARNING 2022-07-04 01:21:44 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

01:21:44.464 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/hg19_All_20180423.vcf.gz -> file:///home/data/references/funcotator_dataSources_LyCEUM/dbsnp/hg19/hg19_All_20180423.vcf.gz

01:21:44.464 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000

01:21:44.563 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/dbsnp/hg19/hg19_All_20180423.vcf.gz

01:21:44.602 INFO  DataSourceUtils - Resolved data source file path: file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/hg19_All_20180423.vcf.gz -> file:///home/data/references/funcotator_dataSources_LyCEUM/dbsnp/hg19/hg19_All_20180423.vcf.gz

01:21:44.755 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/data/references/funcotator_dataSources_LyCEUM/dbsnp/hg19/hg19_All_20180423.vcf.gz

01:21:44.860 INFO  Funcotator - Initializing Funcotator Engine...

01:21:44.973 INFO  FuncotatorUtils - Input VCF has been determined to not based on b37:

01:21:44.973 INFO  FuncotatorUtils -   The following contigs are present in b37 and missing in the input VCF sequence dictionary:

01:21:44.974 INFO  FuncotatorUtils -     1 (len=249250621,assembly=GRCh37)

01:21:44.974 INFO  FuncotatorUtils -     2 (len=243199373,assembly=GRCh37)

01:21:44.974 INFO  FuncotatorUtils -     3 (len=198022430,assembly=GRCh37)

01:21:44.974 INFO  FuncotatorUtils -     4 (len=191154276,assembly=GRCh37)

01:21:44.974 INFO  FuncotatorUtils -     5 (len=180915260,assembly=GRCh37)

01:21:44.974 INFO  FuncotatorUtils -     6 (len=171115067,assembly=GRCh37)

01:21:44.974 INFO  FuncotatorUtils -     7 (len=159138663,assembly=GRCh37)

01:21:44.974 INFO  FuncotatorUtils -     8 (len=146364022,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     9 (len=141213431,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     10 (len=135534747,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     11 (len=135006516,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     12 (len=133851895,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     13 (len=115169878,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     14 (len=107349540,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     15 (len=102531392,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     16 (len=90354753,assembly=GRCh37)

01:21:44.975 INFO  FuncotatorUtils -     17 (len=81195210,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     18 (len=78077248,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     19 (len=59128983,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     20 (len=63025520,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     21 (len=48129895,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     22 (len=51304566,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     X (len=155270560,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     Y (len=59373566,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     MT (len=16569,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     GL000207.1 (len=4262,assembly=GRCh37)

01:21:44.976 INFO  FuncotatorUtils -     GL000226.1 (len=15008,assembly=GRCh37)

01:21:44.977 INFO  FuncotatorUtils -     GL000229.1 (len=19913,assembly=GRCh37)

01:21:44.977 INFO  FuncotatorUtils -     GL000231.1 (len=27386,assembly=GRCh37)

01:21:44.977 INFO  FuncotatorUtils -     GL000210.1 (len=27682,assembly=GRCh37)

01:21:44.977 INFO  FuncotatorUtils -     GL000239.1 (len=33824,assembly=GRCh37)

01:21:44.977 INFO  FuncotatorUtils -     GL000235.1 (len=34474,assembly=GRCh37)

01:21:44.977 INFO  FuncotatorUtils -     GL000201.1 (len=36148,assembly=GRCh37)

01:21:44.978 INFO  FuncotatorUtils -     GL000247.1 (len=36422,assembly=GRCh37)

01:21:44.978 INFO  FuncotatorUtils -     GL000245.1 (len=36651,assembly=GRCh37)

01:21:44.978 INFO  FuncotatorUtils -     GL000197.1 (len=37175,assembly=GRCh37)

01:21:44.978 INFO  FuncotatorUtils -     GL000203.1 (len=37498,assembly=GRCh37)

01:21:44.978 INFO  FuncotatorUtils -     GL000246.1 (len=38154,assembly=GRCh37)

01:21:44.978 INFO  FuncotatorUtils -     GL000249.1 (len=38502,assembly=GRCh37)

01:21:44.979 INFO  FuncotatorUtils -     GL000196.1 (len=38914,assembly=GRCh37)

01:21:44.979 INFO  FuncotatorUtils -     GL000248.1 (len=39786,assembly=GRCh37)

01:21:44.979 INFO  FuncotatorUtils -     GL000244.1 (len=39929,assembly=GRCh37)

01:21:44.979 INFO  FuncotatorUtils -     GL000238.1 (len=39939,assembly=GRCh37)

01:21:44.979 INFO  FuncotatorUtils -     GL000202.1 (len=40103,assembly=GRCh37)

01:21:44.979 INFO  FuncotatorUtils -     GL000234.1 (len=40531,assembly=GRCh37)

01:21:44.980 INFO  FuncotatorUtils -     GL000232.1 (len=40652,assembly=GRCh37)

01:21:44.980 INFO  FuncotatorUtils -     GL000206.1 (len=41001,assembly=GRCh37)

01:21:44.980 INFO  FuncotatorUtils -     GL000240.1 (len=41933,assembly=GRCh37)

01:21:44.980 INFO  FuncotatorUtils -     GL000236.1 (len=41934,assembly=GRCh37)

01:21:44.981 INFO  FuncotatorUtils -     GL000241.1 (len=42152,assembly=GRCh37)

01:21:44.981 INFO  FuncotatorUtils -     GL000243.1 (len=43341,assembly=GRCh37)

01:21:44.981 INFO  FuncotatorUtils -     GL000242.1 (len=43523,assembly=GRCh37)

01:21:44.981 INFO  FuncotatorUtils -     GL000230.1 (len=43691,assembly=GRCh37)

01:21:44.981 INFO  FuncotatorUtils -     GL000237.1 (len=45867,assembly=GRCh37)

01:21:44.982 INFO  FuncotatorUtils -     GL000233.1 (len=45941,assembly=GRCh37)

01:21:44.982 INFO  FuncotatorUtils -     GL000204.1 (len=81310,assembly=GRCh37)

01:21:44.982 INFO  FuncotatorUtils -     GL000198.1 (len=90085,assembly=GRCh37)

01:21:44.982 INFO  FuncotatorUtils -     GL000208.1 (len=92689,assembly=GRCh37)

01:21:44.983 INFO  FuncotatorUtils -     GL000191.1 (len=106433,assembly=GRCh37)

01:21:44.983 INFO  FuncotatorUtils -     GL000227.1 (len=128374,assembly=GRCh37)

01:21:44.983 INFO  FuncotatorUtils -     GL000228.1 (len=129120,assembly=GRCh37)

01:21:44.983 INFO  FuncotatorUtils -     GL000214.1 (len=137718,assembly=GRCh37)

01:21:44.984 INFO  FuncotatorUtils -     GL000221.1 (len=155397,assembly=GRCh37)

01:21:44.984 INFO  FuncotatorUtils -     GL000209.1 (len=159169,assembly=GRCh37)

01:21:44.984 INFO  FuncotatorUtils -     GL000218.1 (len=161147,assembly=GRCh37)

01:21:44.984 INFO  FuncotatorUtils -     GL000220.1 (len=161802,assembly=GRCh37)

01:21:44.984 INFO  FuncotatorUtils -     GL000213.1 (len=164239,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000211.1 (len=166566,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000199.1 (len=169874,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000217.1 (len=172149,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000216.1 (len=172294,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000215.1 (len=172545,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000205.1 (len=174588,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000219.1 (len=179198,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000224.1 (len=179693,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000223.1 (len=180455,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000195.1 (len=182896,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000212.1 (len=186858,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000222.1 (len=186861,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000200.1 (len=187035,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000193.1 (len=189789,assembly=GRCh37)

01:21:44.985 INFO  FuncotatorUtils -     GL000194.1 (len=191469,assembly=GRCh37)

01:21:44.986 INFO  FuncotatorUtils -     GL000225.1 (len=211173,assembly=GRCh37)

01:21:44.986 INFO  FuncotatorUtils -     GL000192.1 (len=547496,assembly=GRCh37)

01:21:44.986 INFO  FuncotatorUtils -     NC_007605 (len=171823,assembly=NC_007605.1)

01:21:44.986 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.

01:21:44.986 INFO  Funcotator - Creating a VCF file for output: file:/home/data/LyCEUM/analysis/lyceum_pipe/MP_22_0027.LyCEUM.SNV.vcf

01:21:45.053 INFO  ProgressMeter - Starting traversal

01:21:45.053 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute

01:21:51.230 INFO  VcfFuncotationFactory - ClinVar_VCF 20180401 cache hits/total: 0/1

01:21:51.230 INFO  VcfFuncotationFactory - cosmic 1 cache hits/total: 0/1

01:21:51.230 INFO  VcfFuncotationFactory - dbSNP 9606_b151 cache hits/total: 0/1

01:21:51.230 INFO  VcfFuncotationFactory - gnomAD_genome 2.1 cache hits/total: 0/1

01:21:51.338 INFO  Funcotator - Shutting down engine

[July 4, 2022 at 1:21:55 AM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.65 minutes.

Runtime.totalMemory()=1041235968

***********************************************************************

 

A USER ERROR has occurred: Input file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic.config must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile

 

***********************************************************************

org.broadinstitute.hellbender.exceptions.UserException: Input file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic.config must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile

at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:580)

at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:363)

at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)

at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.queryFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:314)

at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.getFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:229)

at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:207)

at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:178)

at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:924)

at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:878)

at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)

at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)

at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)

at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)

at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)

at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)

at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)

at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)

at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)

at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)

at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)

at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)

at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

at org.broadinstitute.hellbender.Main.main(Main.java:289)

 

 

 

 

 

I have attempted to index the TSV file using:

$ java -Xmx1024m -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar $LIBPATH/gatk-package-4.2.6.1-local.jar IndexFeatureFile -I mistic_GRCh37.sort.tsv

 

Which resulted in the following error report:

 

01:37:54.996 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/base/lyceum/rlib/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so

01:37:55.151 INFO  IndexFeatureFile - ------------------------------------------------------------

01:37:55.152 INFO  IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.2.6.1

01:37:55.152 INFO  IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/

01:37:55.152 INFO  IndexFeatureFile - Executing as base@basement-b on Linux v4.15.0-188-generic amd64

01:37:55.152 INFO  IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v11.0.15+10-Ubuntu-0ubuntu0.18.04.1

01:37:55.153 INFO  IndexFeatureFile - Start Date/Time: July 4, 2022 at 1:37:54 AM UTC

01:37:55.153 INFO  IndexFeatureFile - ------------------------------------------------------------

01:37:55.153 INFO  IndexFeatureFile - ------------------------------------------------------------

01:37:55.154 INFO  IndexFeatureFile - HTSJDK Version: 2.24.1

01:37:55.154 INFO  IndexFeatureFile - Picard Version: 2.27.1

01:37:55.154 INFO  IndexFeatureFile - Built for Spark Version: 2.4.5

01:37:55.154 INFO  IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2

01:37:55.154 INFO  IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

01:37:55.154 INFO  IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

01:37:55.155 INFO  IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

01:37:55.155 INFO  IndexFeatureFile - Deflater: IntelDeflater

01:37:55.155 INFO  IndexFeatureFile - Inflater: IntelInflater

01:37:55.155 INFO  IndexFeatureFile - GCS max retries/reopens: 20

01:37:55.155 INFO  IndexFeatureFile - Requester pays: disabled

01:37:55.155 INFO  IndexFeatureFile - Initializing engine

01:37:55.155 INFO  IndexFeatureFile - Done initializing engine

01:37:55.158 INFO  IndexFeatureFile - Shutting down engine

[July 4, 2022 at 1:37:55 AM UTC] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.

Runtime.totalMemory()=264241152

***********************************************************************

 

A USER ERROR has occurred: Couldn't read file file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.sort.tsv

 

***********************************************************************

org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read file file:///home/data/references/funcotator_dataSources_LyCEUM/mistic/hg19/mistic_GRCh37.sort.tsv

at org.broadinstitute.hellbender.tools.IndexFeatureFile.doWork(IndexFeatureFile.java:67)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

at org.broadinstitute.hellbender.Main.main(Main.java:289)

 

 

I have attempted to reformat the tsv as a bed file, which can then be indexed; however this file cannot then be properly parsed by Funcotator.

 

I would appreciate your help!