A USER ERROR has occurred: Traversal by intervals was requested but some input files are not indexed

Hi Team,

We are running Cromwell on AWS and running five-dollar-genome-analysis-pipeline-master using GATK toolset. After resolving couple issues related to missing files, NIO etc, we are facing yet another issue related to file indexing during BaseRecalibrator processing.

Can you please help us to identify for missing index files or script which is responsible to index bam files?

Here is error stack trace for your reference.

"A USER ERROR has occurred: Traversal by intervals was requested but some input files are not indexed.

00:46:33
Please index all input files:
Please index all input files:

00:46:33
samtools index /cromwell_root/cromwelleast/cromwell-execution/germline_single_sample_workflow/29c2f87f-54e6-47d3-aa46-b062cee5df57/call-to_bam_workflow/ToBam.to_bam_workflow/3e2283ad-6b4d-4e5d-af68-438f9af13843/call-SortSampleBam/NA12878.aligned.duplicate_marked.sorted.bam
samtools index /cromwell_root/cromwelleast/cromwell-execution/germline_single_sample_workflow/29c2f87f-54e6-47d3-aa46-b062cee5df57/call-to_bam_workflow/ToBam.to_bam_workflow/3e2283ad-6b4d-4e5d-af68-438f9af13843/call-SortSampleBam/NA12878.aligned.duplicate_marked.sorted.bam"

Do let us know if any other information required. Thanks in advance!