Implement.pm line 378 - species-assembly

[acarbome7]

Hello, I’m trying to run the caveman command:

caveman.pl 
-outdir path_to_sample/M417 
-reference path_to_hg38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.fai 
-tumour-bam path_to_tumorBam/867-01-01TD.bam 
-normal-bam path_to_normalBam/867-02-01ND.bam 
-ignore-file path_to_ignore_regions/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment/caveman/flagging/HiDepth_no_Chr.bed 
-tc path_tumor_emptyFile/tumor_CN_emptyFile.txt 
-nc path_tumor_emptyFile/normal_CN_emptyFile.txt 
-td 5 
-nd 2 
-species human 
-species-assembly GRCh38 
-germline-indel path_to_codingexon_indel/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91/vagrent/codingexon_regions_no_chr.indel.bed.gz 
-seqType genome 
-normal-protocol WGS 
-tumour-protocol WGS 
-t 16 
-unmatched-vcf path_to_unmatchedvcf/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment/caveman/unmatchedNormal_no_chr.bed.gz

Problem is I get the error:

Thread xxxx terminated abnormally: Use of uninitialized value in sprintf at /apps/CAVEMANWRAPPER/1.16.0_threads/lib/perl5/Sanger/CGP/Caveman/Implement.pm line 378

Which in the Implement.pm script corresponds to:

$options->{'species-assembly'}

I tried hg38, GRCh38, and 38, but the 3 options give me this same error. I get actually the results, but the tmpFolder is not removed, and I cannot figure out where the problem is.

Here are the modules with the versions I use:

module load pcre2/10.35 gcc/9.2.0 R/4.1.2 perl/5.26.2_threads intel htslib linasm caveman vcftools cavemanpost/1.8.9_threads cgpbigwig pcap-core/5.7.0_threaded cavemanwrapper/1.16.0_threads cgpvcf/2.0.4_threads

I’d appreciate any insights that could help me solve that.

Thanks for your time!

Anna