Error in cgpFlagCaVEMan.pl: Can't use an undefined value as an ARRAY reference...

[larsmew]

I have been using the docker image of cgpwgs v2.1.0 and it's been working great for more than 50 samples. However, I'm getting this issue for one sample when running the cgpFlagCaVEMan command:

Can't use an undefined value as an ARRAY reference at /opt/wtsi-cgp/lib/perl5/Sanger/CGP/CavemanPostProcessor/PostProcessor.pm line 560, <__ANONIO__> line 540.
 at /opt/wtsi-cgp/bin/cgpFlagCaVEMan.pl line 125.
Command exited with non-zero status 2
108.58user 0.85system 1:54.27elapsed 95%CPU (0avgtext+0avgdata 86040maxresident)k
0inputs+0outputs (0major+65360minor)pagefaults 0swaps

Any idea what's gone wrong here?
Let me know if I can provide any further details.

Best,
Lars

[tyoshima]

has there been any updates on this issue? I'm getting the same error for the first time after running cgpwgs v.2.1.0. I also tried cgpwgs v2.1.1 and got the same error

+ /usr/bin/perl /opt/wtsi-cgp/bin/cgpFlagCaVEMan.pl -i /var/spool/results/WGS_N010714-98-A_vs_N010714-4/caveman/tmpCaveman/N010714-98-A_vs_N010714-4.muts.ids.vcfsplit.117 -o /var/spool/results/WGS_N010714-98-A_vs_N010714-4/caveman/tmpCaveman/N010714-98-A_vs_N010714-4.flagged.muts.vcf.117 -s Human -m /var/spool/results/tmp/N010714-98-A.bam -n /var/spool/results/tmp/N010714-4.bam -b /var/spool/ref/caveman/flagging -g /var/spool/results/WGS_N010714-98-A_vs_N010714-4/pindel/N010714-98-A_vs_N010714-4.germline.bed.gz -umv /var/spool/ref/caveman -ref /var/spool/ref/genome.fa.fai -t WGS -sa NCBI38 -c /var/spool/results/flag.vcf.config.WGS.ini -v /var/spool/ref/caveman/flagging/flag.to.vcf.convert.ini -ab /var/spool/ref/vagrent
Can't use an undefined value as an ARRAY reference at /opt/wtsi-cgp/lib/perl5/Sanger/CGP/CavemanPostProcessor/PostProcessor.pm line 560, <__ANONIO__> line 3728.
 at /opt/wtsi-cgp/bin/cgpFlagCaVEMan.pl line 125.
Command exited with non-zero status 2
15.84user 0.28system 0:29.38elapsed 54%CPU (0avgtext+0avgdata 129400maxresident)k
0inputs+0outputs (0major+31768minor)pagefaults 0swaps