#11 CIRI2 test and program fails
Hi,
I tried running test_ciri.pl and got the following error.
This script is used to test CIRI2.
Preparing to test ... Done
Begin Test 1 ...
1..6
ok 1 - Integration test ready
ok 2 - Integration test
End Test 1;
Begin Test 2 ...
ok 3 - Test for 1st scanning ready
ok 4 - Test for 1st scanning
End Test 2;
Begin Test 3 ...
ok 5 - Test for 2nd scanning ready
not ok 6 - Test for 2nd scanning
Failed test 'Test for 2nd scanning'
at test_CIRI.pl line 43.
(in main->test_scanning2)
Structures begin differing at:
$got->{GFGG-GA2-1:2:33:2000:9426 0 2 3} = Does not exist
$expected->{GFGG-GA2-1:2:33:2000:9426 0 2 3} = '1'
Test for 2nd scanning failed.
End Test 3;
Finished 3 testcases.
CIRI2 was tested unsuccessfully.
Looks like you failed 1 test of 6.
Running the script again removed the error. However, later when used the script on real dataset (~10gb bam) I recived the following error in CIRIerror.log
"Thread 2 terminated abnormally: Range iterator outside integer range at CIRI2.pl line 1665, <in> line 280269."</in>
I am not using multi threading option to run on real data. Can you provide a solution for this issue?
Thanks
Regards,
Kandarp
Hi Kandarp,
We never met that situation before. Did you use parallel Perl 5.8 or higher? Could you please also let me see the lines around line 280,269 of the sam file that you input?
Thanks,
Yuan