virusbreakend docker image issue: BAM index not found

[ugh-astya]

Hi, I am trying to run virus breakend on bwa mem output (it is a sorted bam file). I have generated the bam index using samtools index. I pulled gridss image using docker pull gridss/gridss:latest Then I enter the docker image through docker run -v $(pwd):/home/bleh -it gridss/gridss:latest

Next, I run virusbreakend: virusbreakend --kraken2db /home/bleh/virusbreakenddb_20210401 --output output.vcf --reference /home/bleh/fastvifi_ref/data_repo/hg19/hg19full.fa -j /home/bleh/gridss-2.13.2-gridss-jar-with-dependencies.jar /home/bleh/data/hg19_map/sortbwaB5.bam

I get the following error after the calling structural variants step:

Exit status 0 for $timecmd gridss -w $adjusteddir -t $threads -r $prefix_adjusted.viral.fa -j $gridss_jar -o $file_gridss_vcf -a $file_assembly -c $file_gridss_configuration --maxcoverage $maxcoverage $gridssargs $bam_list_args 1>&2 2>> $logfile

See log file ./output.vcf.virusbreakend.working/virusbreakend.20230902_090310.ef4dd93274b1.10.log for underlying error

virusbreakend.20230902_090310.ef4dd93274b1.10.log

The above log file asks me to refer to another log file at ./output.vcf.virusbreakend.working/adjusted/gridss.full.20230902_090418.ef4dd93274b1.1155.log gridss.full.20230902_090418.ef4dd93274b1.1155.log

Inside this log file it says at line 307

ERROR   2023-09-02 09:04:22 VariantCaller   Fatal error during breakpoint identification 
java.util.concurrent.ExecutionException: htsjdk.samtools.SAMException: No index is available for this BAM file.

But I have already created the bam index. I have modified the permissions of the index file as well with chmod 777 Any help is much appreciated.