Missing/Incomplete VCF meta information (header)

I have a bam file from BWA mem, I then run the following clever command:

clever --use_xa --sorted input.bam reference.fasta result-directory

I run picard RenameSampleInVcf:

picard RenameSampleInVcf I=predictions.vcf O=clever.vcf NEW_SAMPLE_NAME="clever"

I get the following error:

Exception in thread "main" htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 5: The reference allele cannot be missing, for input source:

The predicted VCF (first 10 lines) looks like this:

head predictions.vcf

##fileformat=VCFv4.1
##fileDate=20190408
##source=clever-postprocessing-v2.4 cmdline: /exports/sascstudent/cedrick/conda/envs/vcf_parser/bin/postprocess-predictions --vcf --covbal 0.333 --stddev 149.505000 /exports/sascstudent/cedrick/wdl/clevertest/predictions.raw.txt 266.394000
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  default
chr1    279029  L30712  .       <DEL>   .       PASS    IMPRECISE;SVTYPE=DEL;SVLEN=-434;BPWINDOW=278975,279518;CILEN=328,540;ESUPPORT=2.000000  GT:DP   1/.:2
chr1    444858  L30618  .       <DEL>   .       PASS    IMPRECISE;SVTYPE=DEL;SVLEN=-384;BPWINDOW=444859,445242;CILEN=278,490;ESUPPORT=2.000000  GT:DP   1/.:2
chr1    591635  L29626  .       <DEL>   .       PASS    IMPRECISE;SVTYPE=DEL;SVLEN=-397;BPWINDOW=591636,592032;CILEN=291,503;ESUPPORT=2.000000  GT:DP   1/.:2
chr1    635879  L32898  .       <DEL>   .       PASS    IMPRECISE;SVTYPE=DEL;SVLEN=-134;BPWINDOW=635880,636013;CILEN=72,196;ESUPPORT=6.000000   GT:DP   1/.:6
chr1    689898  L29815  .       <DEL>   .       PASS    IMPRECISE;SVTYPE=DEL;SVLEN=-469;BPWINDOW=689827,690440;CILEN=363,575;ESUPPORT=2.000000  GT:DP   1/.:2
chr1    738806  L31972  .       <DEL>   .       PASS    IMPRECISE;SVTYPE=DEL;SVLEN=-287;BPWINDOW=738807,739093;CILEN=220,354;ESUPPORT=5.000000  GT:DP   1/.:5

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