Problem preping stats from bam files ONCOCNV_getCounts.pl line 450

[kmavrommatis]

Hi,
I am using OncoCNV 6.6 to get copy number estimates on exome data.
There is an error that comes up when running the ONCOCNV_getCounts.pl

$perl $TOOLDIR/ONCOCNV_getCounts.pl getControlStats -m Exon -b $targetBed -c $controls -o $OUTDIR/Control.stats.txt

reading NA12891_Capture.MarkDuplicates.mdup..GATK.Recalibrate.bam
	sample name: NA12891_Capture.MarkDuplicates.mdup..GATK.Recalibrate

[ many lines counting reads ]
read 95700000 reads
	Total target length: 0
processed 2 controls, NA12878_Capture.MarkDuplicates.mdup..GATK.Recalibrate NA12891_Capture.MarkDuplicates.mdup..GATK.Recalibrate
Can't use an undefined value as an ARRAY reference at
	/opt/ONCOCNV-6.6/src//ONCOCNV_getCounts.pl line 450 (#1)
    (F) A value used as either a hard reference or a symbolic reference must
    be a defined value.  This helps to delurk some insidious errors.
    
Uncaught exception from user code:
	Can't use an undefined value as an ARRAY reference at /opt/ONCOCNV-6.6/src//ONCOCNV_getCounts.pl line 450.

the input files are :
bed file with the exome target regions

$head 1-target.bed 
chr1	12100	12258	AMPLENSG00000223972.4	0	ENSG00000223972.4
chr1	12555	12721	AMPLENSG00000223972.4.1	0	ENSG00000223972.4
chr1	13333	13701	AMPLENSG00000223972.4.2	0	ENSG00000223972.4
chr1	30336	30503	AMPLENSG00000243485.2	0	ENSG00000243485.2
chr1	35047	35544	AMPLENSG00000237613.2	0	ENSG00000237613.2
chr1	35620	35778	AMPLENSG00000237613.2.1	0	ENSG00000237613.2
chr1	69091	70008	AMPLENSG00000186092.4	0	ENSG00000186092.4
chr1	324296	324394	AMPLENSG00000237094.6	0	ENSG00000237094.6
chr1	324429	325605	AMPLENSG00000237094.6.1	0	ENSG00000237094.6
chr1	327736	328214	AMPLENSG00000237094.6.2	0	ENSG00000237094.6

and a bam file processed with Picard MarkDuplicates, GATK Realign and Recalibrate.
Before any processing since the BAM file contains aligned reads to unplaced scaffolds which are not present in the target.bed I am filtering with samtools -L <target.bed>

Any advice/help/suggestions are welcome
Thanks
Konstantinos

[jiao2017]

I meet this error too in 6.8 version
Total target length: 43760
processed 4 controls, D4_chr D5_chr D6_chr D8_chr
Can't use an undefined value as an ARRAY reference at
software/oncocnv/ONCOCNV-6.8/src//ONCOCNV_getCounts_b37.pl line 452 (#1)
(F) A value used as either a hard reference or a symbolic reference must
be a defined value. This helps to delurk some insidious errors.

Uncaught exception from user code:
Can't use an undefined value as an ARRAY reference at software/oncocnv/ONCOCNV-6.8/src//ONCOCNV_getCounts_b37.pl line 452