Ikram Ullah
While trying to run QCFasta component, in the pipeline somewhere, the QCParser.pl perl file appears to be failing to include componentSkeleton.pm file. I checked the componentSkeleton.pm file in my installation and can locate it in ./anduril2/utils/perl/componentSkeleton.pm.
Do we need to (re)set the include paths somewhere in the above perl code?
Here is the log from log_/qc-QCFasta-apply-overRepSeq_2
Log started on 2015-05-18 18:52:12;
Executing qc-QCFasta-apply-overRepSeq_2 (anduril.sequencing.QCParser) (QCFasta.scala:382)
[STDERR qc-QCFasta-apply-overRepSeq_2] Can't locate componentSkeleton.pm in @INC (you may need to install the componentSkeleton module) (@INC contains: /Users/K7-IKRULL-M/Documents/KS_Stuff/anduril2/perl /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Users/K7-IKRULL-M/Documents/KS_Stuff/anduril2/bundles/sequencing/components/QCParser/QCParser.pl line 4.
[STDERR qc-QCFasta-apply-overRepSeq_2] BEGIN failed--compilation aborted at /Users/K7-IKRULL-M/Documents/KS_Stuff/anduril2/bundles/sequencing/components/QCParser/QCParser.pl line 4.
[ERROR] anduril.sequencing.QCFasta$Implementation$.CheckQC(QCFasta.scala:382), Component qc-QCFasta-apply-overRepSeq_2: Component returned error status: 2
[ERROR] anduril.sequencing.QCFasta$Implementation$.CheckQC(QCFasta.scala:382), Component qc-QCFasta-apply-overRepSeq_2: Error reading array index produced by: java.io.FileNotFoundException: /Users/K7-IKRULL-M/Documents/KS_Stuff/anduril2/my_examples/result_/qc-QCFasta-apply-overRepSeq_2/basicStats/_index (No such file or directory)
Component qc-QCFasta-apply-overRepSeq_2 (QCFasta.scala:382) finished with failure; READY queue: qc-QCFasta-preStats_n1
Log closed on 2015-05-18
