Error: Can't parse sequence for chromosome chr#

[mglgc]

Hi,
After a successful starting command
'docker run -v /home/james/parliament2/:/home/dnanexus/in/ -v /home/jameso/parliament2/outputs/:/home/dnanexus/out dnanexus/parliament2:latest --bam test_sarek.bam --bai test_sarek.bai -r GRCh37.chr.p13.genome.fa --fai GRCh37.chr.p13.genome.fa.fai --breakdancer --cnvnator --manta --genotype --svviz'

several error messages are displayed:
Convert CNVnator results to VCF format
Reading calls ...
Can't parse sequence for chromosome chr1.
Can't parse sequence for chromosome chr2.
Can't parse sequence for chromosome chr3.
Traceback (most recent call last):
File "/BreakDancer2Merge.py", line 88, in
if int(data[h["Score"]]) <= 50:
IndexError: list index out of range
Can't parse sequence for chromosome chr4.
...and so on for all the chromosomes.

Please, some help will be welcome. Thank you in advance for replying