charite/jannovar

Building hg38/ensembl version 105 results in NPE

znikasz opened this issue · 0 comments

Describe the bug
I get NPE when building hg38/ensembl version 105

To Reproduce
Create default_sources.ini with:

[hg38/ensembl]
type=ensembl
alias=MT,M,chrM
chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz
chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.109/Assembled_chromosomes/chr_accessions_GRCh38.p12
chrToAccessions.format=chr_accessions
gtf=http://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.gtf.gz
cdna=http://ftp.ensembl.org/pub/release-105/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
table_gene_main=http://ftp.ensembl.org/pub/release-105/mysql/ensembl_mart_105/hsapiens_gene_ensembl__gene__main.txt.gz
table_hgnc=http://ftp.ensembl.org/pub/release-105/mysql/ensembl_mart_105/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz
table_entrezgene=http://ftp.ensembl.org/pub/release-105/mysql/ensembl_mart_105/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz

And run:

java -jar jannovar-cli-0.38.jar download -s  default_sources.ini -d hg38/ensembl

What you get is NPE error:

....
INFO Assigning additional HGNC information to transcripts..
INFO Adding sequence information from cdna FASTA...
INFO Ignoring 60049 transcripts without sequence.
INFO Successfully processed 184717 transcripts with sequence.
INFO Finalising TranscriptModels...
INFO Built 184717 TranscriptModels
Exception in thread "main" java.lang.NullPointerException: null key in entry: null=ENST00000541353.2(12:g.63682523_63715476)
        at com.google.common.collect.CollectPreconditions.checkEntryNotNull(CollectPreconditions.java:32)
        at com.google.common.collect.ImmutableMultimap$Builder.put(ImmutableMultimap.java:168)
        at de.charite.compbio.jannovar.data.JannovarData.makeTMByGeneSymbol(JannovarData.java:100)
        at de.charite.compbio.jannovar.data.JannovarData.<init>(JannovarData.java:60)
        at de.charite.compbio.jannovar.datasource.JannovarDataFactory.build(JannovarDataFactory.java:108)
        at de.charite.compbio.jannovar.cmd.download.DownloadCommand.run(DownloadCommand.java:43)
        at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:74)

Expected behavior
I'd like to get ser file, without NPE