Error: can't undefined value as an ARRAY reference at detect_cnv.pl

[SamGreen52]

Hello!
For a few of my samples I keep getting this error message without it reporting any data:

NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file Signals_Complete_Final/Complete_RawCNV-logs/206.log
NOTICE: Recalling CNVs for trio: Signals_Complete_Final/207166290026_R01C02 Signals_Complete_Final/207166290026_R02C02 Signals_Complete_Final/207166290026_R04C02
NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from hg_38.pfb ... Done with 651801 records (1484742 records in chr 0,MT,XY were discarded)
NOTICE: Total of 112 CNV regions will be validated by family information (Signals_Complete_Final/207166290026_R01C02 Signals_Complete_Final/207166290026_R02C02 Signals_Complete_Final/207166290026_R04C02)
NOTICE: Reading LRR and BAF values for from Signals_Complete_Final/207166290026_R01C02 ... Done with 651801 records in 24 chromosomes (2226 records are discarded due to lack of PFB information for the markers)
NOTICE: Data from chromosome X,Y will not be used in analysis
NOTICE: Median-adjusting LRR values for all autosome markers from Signals_Complete_Final/207166290026_R01C02 by 0.0069
NOTICE: Median-adjusting BAF values for all autosome markers from Signals_Complete_Final/207166290026_R01C02 by -0.0031
NOTICE: quality summary for Signals_Complete_Final/207166290026_R01C02: LRR_mean=-0.0078 LRR_median=0.0000 LRR_SD=0.1091 BAF_mean=0.5015 BAF_median=0.5000 BAF_SD=0.0337 BAF_DRIFT=0.000055 WF=-0.0271 GCWF=-0.0239
Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843.
Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843.
Use of uninitialized value in string eq at detect_cnv.pl line 1849.
Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843.
Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843.
Use of uninitialized value in string eq at detect_cnv.pl line 1849.
Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843.
Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843.
Use of uninitialized value in string eq at detect_cnv.pl line 1849.
Can't use an undefined value as an ARRAY reference at detect_cnv.pl line 509.
Any suggestions?

[kaichop]

This looks like a validation CNV calling procedure. In some cases, the markers in father, mother and offspring are not identical which can cause mismatch in validation calls. Can you confirm if they have identical lines (markers)?

…

On Thu, Jun 13, 2024 at 3:29 PM Sam Greenspun ***@***.***> wrote: Hello! For a few of my samples I keep getting this error message without it reporting any data: NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file Signals_Complete_Final/Complete_RawCNV-logs/206.log NOTICE: Recalling CNVs for trio: Signals_Complete_Final/207166290026_R01C02 Signals_Complete_Final/207166290026_R02C02 Signals_Complete_Final/207166290026_R04C02 NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from hg_38.pfb ... Done with 651801 records (1484742 records in chr 0,MT,XY were discarded) NOTICE: Total of 112 CNV regions will be validated by family information (Signals_Complete_Final/207166290026_R01C02 Signals_Complete_Final/207166290026_R02C02 Signals_Complete_Final/207166290026_R04C02) NOTICE: Reading LRR and BAF values for from Signals_Complete_Final/207166290026_R01C02 ... Done with 651801 records in 24 chromosomes (2226 records are discarded due to lack of PFB information for the markers) NOTICE: Data from chromosome X,Y will not be used in analysis NOTICE: Median-adjusting LRR values for all autosome markers from Signals_Complete_Final/207166290026_R01C02 by 0.0069 NOTICE: Median-adjusting BAF values for all autosome markers from Signals_Complete_Final/207166290026_R01C02 by -0.0031 NOTICE: quality summary for Signals_Complete_Final/207166290026_R01C02: LRR_mean=-0.0078 LRR_median=0.0000 LRR_SD=0.1091 BAF_mean=0.5015 BAF_median=0.5000 BAF_SD=0.0337 BAF_DRIFT=0.000055 WF=-0.0271 GCWF=-0.0239 Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843. Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843. Use of uninitialized value in string eq at detect_cnv.pl line 1849. Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843. Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843. Use of uninitialized value in string eq at detect_cnv.pl line 1849. Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843. Use of uninitialized value in subtraction (-) at detect_cnv.pl line 1843. Use of uninitialized value in string eq at detect_cnv.pl line 1849. Can't use an undefined value as an ARRAY reference at detect_cnv.pl line 509. Any suggestions? — Reply to this email directly, view it on GitHub <#121>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OBXSYTGUMJFDZMAUUTZHHXILAVCNFSM6AAAAABJJATQZCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM2TCOJQGU4TIMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>