On Thu, Jun 27, 2013 at 2:18 PM, Karl Ward kw1213@nyu.edu wrote:
The errors I describe below may or may not be significant. As I mentioned to Ashish, I am not confident that Illumina's CASAVA validation process is robust. However, it is worth noting that our installs of CASAVA do not pass validation on either Rabbot or Bowery. This may merit further investigation.
I just installed CASAVA 1.8.2 on Rabbot, in case we need it there. I ran the first validation dataset, described in the attached CASAVA 1.8.2 Customer Release Notes as "end-to-end validation on the DNA (small) test data set." I got the following results:
On Thu, Jun 27, 2013 at 2:18 PM, Karl Ward kw1213@nyu.edu wrote: The errors I describe below may or may not be significant. As I mentioned to Ashish, I am not confident that Illumina's CASAVA validation process is robust. However, it is worth noting that our installs of CASAVA do not pass validation on either Rabbot or Bowery. This may merit further investigation.
I just installed CASAVA 1.8.2 on Rabbot, in case we need it there. I ran the first validation dataset, described in the attached CASAVA 1.8.2 Customer Release Notes as "end-to-end validation on the DNA (small) test data set." I got the following results:
$ cat ValidationDefault/ValidationSummary.txt Demux.diff validation [PASS] Alignment.diff validation [FAIL] Build.diff validation [PASS]
I ran the second validation data set, described as "end-to-end validation on the indexed RNA (large) test data set" and got the following results:
$ cat ValidationMultiplexed/ValidationSummary.txt Demux.diff validation [FAIL] Alignment.diff validation [FAIL] Build.diff validation [PASS]
Out of curiosity, I ran these same validations on Bowery. Worse than Rabbot, on Bowery the DNA validation did not complete:
[2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] perl: symbol lookup error: /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/perlchartdir510i64mt.so: undefined symbol: Perl_Gthr_key_ptr [2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] [configureBuild.pl] ERROR:In /share/apps/casava/1.8.2/intel/libexec/CASAVA-1.8.2/generateReports.pl --projectDir=/scratch/kw1213/tmp/ValidationDefault/Build/Project_FC626BWAAXX/Sample_lane4 --target=configure - See errors above [2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured]
[2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] [configureBuild.pl] BACKTRACE: at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/Common/IOLib.pm line 205 [2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::Common::IOLib::executeCmdEx('/share/apps/casava/1.8.2/intel/libexec/CASAVA-1.8.2/generateR...', 1, 4) called at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/Common/IOLib.pm line 165 [2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::Common::IOLib::executeCmd('/share/apps/casava/1.8.2/intel/libexec/CASAVA-1.8.2/generateR...', 4) called at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/PostAlignment/Sequencing/Config.pm line 377 [2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::PostAlignment::Sequencing::Config::configureBuild('ARRAY(0xcc2bde8)', '/scratch/kw1213/tmp/ValidationDefault/Build/Project_FC626BWAA...', 1) called at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/PostAlignment/Sequencing/Config.pm line 435 [2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::PostAlignment::Sequencing::Config::configureTargets(0, 'ARRAY(0xcc2be78)', 'ARRAY(0xcc2bde8)', '/scratch/kw1213/tmp/ValidationDefault/Build/Project_FC626BWAA...') called at /share/apps/casava/1.8.2/intel/bin/configureBuild.pl line 338 [2013-06-27 14:05:51] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Died at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/Common/Log.pm line 310. make: *\ [Build/Project_FC626BWAAXX/Sample_lane4/Build.configured] Error 2 make: Leaving directory `/scratch/kw1213/tmp/ValidationDefault'
The indexed RNA validation also did not complete:
[2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] perl: symbol lookup error: /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/perlchartdir510i64mt.so: undefined symbol: Perl_Gthr_key_ptr [2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] [configureBuild.pl] ERROR:In /share/apps/casava/1.8.2/intel/libexec/CASAVA-1.8.2/generateReports.pl --projectDir=/scratch/kw1213/tmp/ValidationMultiplexed/Build/Project_FC626BWAAXX/Sample_lane4 --target=configure - See errors above [2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured]
[2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] [configureBuild.pl] BACKTRACE: at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/Common/IOLib.pm line 205 [2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::Common::IOLib::executeCmdEx('/share/apps/casava/1.8.2/intel/libexec/CASAVA-1.8.2/generateR...', 1, 4) called at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/Common/IOLib.pm line 165 [2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::Common::IOLib::executeCmd('/share/apps/casava/1.8.2/intel/libexec/CASAVA-1.8.2/generateR...', 4) called at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/PostAlignment/Sequencing/Config.pm line 377 [2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::PostAlignment::Sequencing::Config::configureBuild('ARRAY(0xcfb6de8)', '/scratch/kw1213/tmp/ValidationMultiplexed/Build/Project_FC626...', 1) called at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/PostAlignment/Sequencing/Config.pm line 435 [2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Casava::PostAlignment::Sequencing::Config::configureTargets(0, 'ARRAY(0xcfb6e78)', 'ARRAY(0xcfb6de8)', '/scratch/kw1213/tmp/ValidationMultiplexed/Build/Project_FC626...') called at /share/apps/casava/1.8.2/intel/bin/configureBuild.pl line 338 [2013-06-27 14:12:26] [compute-12-1.local] [/Project_FC626BWAAXX/Sample_lane4/Build.configured] Died at /share/apps/casava/1.8.2/intel/lib/CASAVA-1.8.2/perl/Casava/Common/Log.pm line 310. make: *\ [Build/Project_FC626BWAAXX/Sample_lane4/Build.configured] Error 2 make: Leaving directory `/scratch/kw1213/tmp/ValidationMultiplexed'