Non-parallel IndelRealigner sometimes fails

[julia326]

Example error message (strangely the file mentioned there is the output file, not the input):

##### ERROR AN INPUT FILE ERROR has occurred (version 3.7-0-gcfedb67): 
##### ERROR
##### ERROR This means that there is something wrong with the input file(s) you provided.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum until you have followed these instructions:
##### ERROR - Make sure that your BAM file is well-formed by running Picard's validator on it
##### ERROR (see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)
##### ERROR - Ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'
##### ERROR - Ensure that your CRAM index is not corrupted: delete the current one and regenerate it with
##### ERROR 'java -jar cramtools-3.0.jar index --bam-style-index --input-file <input cram file> --reference-fasta-file <reference fasta file>'
##### ERROR (see https://github.com/enasequence/cramtools/tree/v3.0 for details)
##### ERROR
##### ERROR MESSAGE: Terminator block not found after closing BGZF file tumor_aligned_coordinate_sorted_dups_indelreal_chr_ALL.bam