Error: Unknown option '-noCheckCds'

[tania-k]

Describe the issue
Hello folks,
Thank you for creating an important tool to help breakdown VCF results.
I have an issue that has popped up and I am unsure how to progress as it doesn't seem to be an issue that genuinely makes sense.

I have snpeff/4.3t loaded into my university cluster as a module along with a separate conda environment with snpeff/4.3t but I am receiving the same issue.
It is an error involving the build option, -noCheckCds and -noCheckProtein where these options don't seem to exist? I've tried different versions of snpeff and I am receiving the same error. I am not sure what I am missing? I am running snpeff build on a custom more up-to-date genome of Histoplasma capsulatum.

Here is the script I ran:
java -Xmx64g -jar /nas/longleaf/apps/snpeff/4.3q/snpEff/snpEff.jar build -datadir snpeff/data -c /nas/longleaf/home/taniak/taniak/Histo_PopGenomics/snpeff/snpEff.config -gff3 -noCheckCds -noCheckProtein -nodownload -v Histoplasma_capsulatum_WU24

Here is the error log I am receiving.

GFF is Histoplasma_capsulatum_WU24.gff3
genome/FungiDB-67_HcapsulatumWU24_Genome.fasta
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'build'
Error: Unknown option '-noCheckCds'

snpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
Usage: snpEff build [options] genome_version

Build DB options:
Database format option (default: Auto detect):
-embl : Use Embl format.
-genbank : Use GenBank format.
-gff2 : Use GFF2 format (obsolete).
-gff3 : Use GFF3 format.
-gtf22 : Use GTF 2.2 format.
-knowngenes : Use KnownGenes table from UCSC.
-refseq : Use RefSeq table from UCSC.

Database build options:
-cellType : Only build regulation tracks for cellType .
-noStoreSeqs : Do not store sequence in binary files. Default: true
-onlyReg : Only build regulation tracks.
-regSortedByType : The 'regulation.gff' file is sorted by 'regulation type' instead of sorted by chromosome:pos. >Default: false
-storeSeqs : Store sequence in binary files. Default: false

Generic options:
-c , -config : Specify config file
-configOption name=value : Override a config file option
-d , -debug : Debug mode (very verbose).
-dataDir : Override data_dir parameter from config file.
-download : Download a SnpEff database, if not available locally. Default: false
-nodownload : Do not download a SnpEff database, if not available locally.
-h , -help : Show this help and exit
-noLog : Do not report usage statistics to server
-t : Use multiple threads (implies '-noStats'). Default 'off'
-q , -quiet : Quiet mode (do not show any messages or errors)
-v , -verbose : Verbose mode
-version : Show version number and exit

java -Xmx64g -jar /nas/longleaf/apps/snpeff/4.3t/snpEff/snpEff.jar eff -c >/nas/longleaf/home/taniak/taniak/Histo_PopGenomics/snpEff/snpEff.config -dataDir >/nas/longleaf/home/taniak/taniak/Histo_PopGenomics/snpEff/data -v Histoplasma_capsulatum_WU24 >WU24_v1.All.allvariants_combined_selected.vcf > WU24_v1.All.snpEff.vcf

00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'eff'
00:00:00 Reading configuration file '/nas/longleaf/home/taniak/taniak/Histo_PopGenomics/snpEff/snpEff.config'. Genome: >'Histoplasma_capsulatum_WU24'
00:00:00 Reading config file: /work/users/t/a/taniak/Histo_PopGenomics/snpEff/snpEff.config
00:00:00 done
00:00:00 Reading database for genome version 'Histoplasma_capsulatum_WU24' from file >'/nas/longleaf/home/taniak/taniak/Histo_PopGenomics/snpEff/data/Histoplasma_capsulatum_WU24/snpEffectPredictor.bin' (this >might take a while)
java.lang.RuntimeException: ERROR: Cannot read file >'/nas/longleaf/home/taniak/taniak/Histo_PopGenomics/snpEff/data/Histoplasma_capsulatum_WU24/snpEffectPredictor.bin'.
You can try to download the database by running the following command:
java -jar snpEff.jar download Histoplasma_capsulatum_WU24

at org.snpeff.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:62)
at org.snpeff.snpEffect.Config.loadSnpEffectPredictor(Config.java:579)
at org.snpeff.SnpEff.loadDb(SnpEff.java:520)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:00 Logging
00:00:01 Checking for updates...
00:00:02 Done.
Failed to open WU24_v1.All.snpEff.vcf: unknown file type

It is clear the database is not being created as it's giving me the error. I have also run it without the two flags, it claims the database is built, but there is no output file snpEffectPredictor.bin so I don't think it's doing this correctly.
Thank you for your time!
Tania Kurbessoian, Ph.D.