pcingola
Error: Unknown option '-noCheckCds'
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.
