Amber Config and Sequence index Errors

[weewus]

I'm trying to run the following:

java -jar jarfiles/amber_v4.0.1.jar com.hartwig.hmftools.amber.AmberApplication
-reference
-reference_bam .cram
-tumor
-tumor_bam .cram
-output_dir outdir
-loci AmberGermlineSites.38.tsv.gz
-ref_genome GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta
-ref_genome_version 38

14:39:38.292 [ERROR] expecting config name but encountered invalid argument: com.hartwig.hmftools.amber.AmberApplication

I receive this error and am a little confused as to why.

I have tried running the same with java -cp, and the program runs, but I instead get errors like these:
14:28:16.031 [ERROR] cannot find sequence index for chromosome 11 in bam header
while running

for many chromosomes

Is this to do with using cram files as opposed to bam files?
Is there any more information I can provide to better describe this issue?

Thanks,
Andreas

[weewus]

It seems com.hartwig.hmftools.amber.AmberApplication is deprecated the command java -jar jarfiles/amber_v4.0.1.jar should just be run with the relevant options