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BoevaLab / ONCOCNV

ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data
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Problem preping stats from bam files ONCOCNV_getCounts.pl line 450 #5

Open kmavrommatis opened 7 years ago

kmavrommatis commented 7 years ago

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

Any advice/help/suggestions are welcome Thanks Konstantinos

jiao2017 commented 6 years ago

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