java.base/java.lang.Double cannot be cast to java.base/java.lang.Integer

[Aworwui]

I'm runing vigor with sarscov2 ref database name and get this error message below: Command line arguments: -i fastp_report/assembly_out/023/023_contigs.fasta -o ./annot/023_annot -d sarscov2 -c 90 Current working directory: rwui/covid alignment_module exonerate (defaults) alignment_score_factor 1.0 (/shared/software/VIGOR_DB/Reference_DBs/sarscov2_db.ini) circular_genome false (commandline) exonerate_path xonerate-2.2.0/bin/exonerate (/shared/software/vigor-4.1.2/config/vigor.ini) frameshift_sensitivity 1 (commandline) leakystop_notFound_score 80.0 (defaults) leakystop_score_factor 1.0 (/shared/software/VIGOR_DB/Reference_DBs/sarscov2_db.ini) locustag vigor (commandline) mature_pep_mincoverage 50.0 (defaults) mature_pep_minidentity 25.0 (defaults) mature_pep_minsimilarity 40.0 (defaults) max_aa_overlap 10 (defaults) max_align_merge_aa_gap 10 (defaults) max_gene_overlap 50 (/shared/software/VIGOR_DB/Reference_DBs/sarscov2_db.ini) max_intron_size 2500 (defaults) max_nt_overlap 30 (defaults) min_gene_coverage 10.0 (commandline) min_missing_AA_size 10 (defaults) min_pseudogene_coverage 80.0 (defaults) min_pseudogene_identity 70.0 (defaults) min_pseudogene_similarity 80.0 (defaults) min_seq_gap_length 20 (defaults) output_directory covid/./annot (commandline) output_formats [ALN, CDS, PEP, GFF3, TBL] (defaults) output_prefix 023_annot (commandline) reference_database_file VIGOR_DB/Reference_DBs/sarscov2_db (commandline) reference_database_path /VIGOR_DB/Reference_DBs (/shared/software/vigor-4.1.2/config/vigor.ini) splicing_score_factor 1.0 (/shared/software/VIGOR_DB/Reference_DBs/sarscov2_db.ini) start_codon_search_window 50 (defaults) start_codons [ATG] (defaults) start_score_factor 1.0 (/shared/software/VIGOR_DB/Reference_DBs/sarscov2_db.ini) stop_codon_search_window 50 (defaults) stop_score_factor 1.0 (/shared/software/VIGOR_DB/Reference_DBs/sarscov2_db.ini) temporary_directory /tmp/vigor-temp (/shared/software/vigor-4.1.2/config/vigor.ini) verbose false (commandline) Getting alignments for NODE_1_length_1076_cov_5576.461461 1 alignment(s) found for sequence NODE_1_length_1076_cov_5576.461461 1 candidate model(s) found for sequence NODE_1_length_1076_cov_5576.461461 Exception encountered: exiting 1 java.lang.ClassCastException: java.base/java.lang.Double cannot be cast to java.base/java.lang.Integer at org.jcvi.vigor.service.GeneModelGenerationService.filterModelsWithStructuralSpecifications(GeneModelGenerationService.java:225) ~[vigor-4.1.20190809-171720-7fa683e-jar-with-dependencies.jar:?] at org.jcvi.vigor.service.GeneModelGenerationService.generateGeneModel(GeneModelGenerationService.java:67) ~[vigor-4.1.20190809-171720-7fa683e-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.generateGeneModels(Vigor.java:395) ~[vigor-4.1.20190809-171720-7fa683e-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.modelsFromNucleotideRecord(Vigor.java:297) ~[vigor-4.1.20190809-171720-7fa683e-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.generateAnnotations(Vigor.java:240) ~[vigor-4.1.20190809-171720-7fa683e-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.run(Vigor.java:87) [vigor-4.1.20190809-171720-7fa683e-jar-with-dependencies.jar:?] at org.jcvi.vigor.Application.main(Application.java:12) [vigor-4.1.20190809-171720-7fa683e-jar-with-dependencies.jar:?]

please help

[Aworwui]

suspect the error is coming from this line int min_coverage = config.getOrDefault(ConfigurationParameters.GeneMinimumCoverage, 0); line 225 in GeneModelGenerationService.java

[jchriste-jcvi]

Thanks for the feedback! I'll take a look at it and let you know what I find.

[jchriste-jcvi]

I pushed the fix that changes that int to a double in that line. Thanks for the bug report. I'll close this when I add a test.

[jchriste-jcvi]

Close fixed bugs.