Hello @liangkaiye. I am getting a segfault using pindel + breakdancer. All other events are output by pindel except for these:

-rw-r--r-- 1 apand2 mdclab 0 Aug 11 12:42 LB_BGI_vs_none.pindel_BP
-rw-r--r-- 1 apand2 mdclab 0 Aug 11 12:42 LB_BGI_vs_none.breakdancer.pindel.txt --> (--output_of_breakdancer_events)
-rw-r--r-- 1 apand2 mdclab 0 Aug 11 12:42 LB_BGI_vs_none.pindel_CloseEndMapped

Looking at the coredump:

Segfault happened @ 889

884     bool BDData::isBreakDancerEvent( const unsigned int leftPosition, const unsigned int rightPosition ) const
885     {
886        unsigned int rawLeftPosition = leftPosition + g_SpacerBeforeAfter;
887        unsigned int rawRightPosition = rightPosition + g_SpacerBeforeAfter;
888
889        if ( m_breakDancerMask[ rawLeftPosition - m_currentWindow.getStart() ]!=0  &&
890                       m_breakDancerMask[ rawRightPosition - m_currentWindow.getStart() ]!=0 ) {
891                     //std::cout << "Found breakdancerEvent near " << leftPosition << "-" << rightPosition << "\n";
892          
893                     return haveCommonBDEvent( m_regionsToScanCollection[ m_breakDancerMask[ rawLeftPosition - m_currentWindow.getStart() ] ],

rawLeftPosition = 4239970296

p m_currentWindow.m_currentStart
$4 = 55097000

m_breakDancerMask[rawLeftPosition - 55097000 ]
   Cannot access memory at address 0x4481665c0

(gdb) p m_breakDancerMask[rawLeftPosition ]
Cannot access memory at address 0x455394060

That looks to be the start of the problem.

m_breakDancerMask[ 4239970296 - 55097000 ]

Have you seen this before? I am currently using (Pindel version 0.2.5a4, May 2 2014.), Is there a specific version of breakdancer I should use too?

Also, I updated pindel to 0.2.5a7 and ran wihout the breakdancer output. It went further than before but I eventually get this error:

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
/opt/gridengine/default/spool/compute-1-2/job_scripts/177954: line 112: 21543 Aborted                 pindel -T $THREADS -f $REF -i $PINDEL_CFG -c ALL --report_inversions --report_duplications --report_long_insertions --report_breakpoints --report_interchromosomal_events -o $ANALYSIS_OUT_DIR/$ANALYSIS_OUT_DIR_NAME.pindel

Hi liangkaiye,

I also have a segfault in this function, with 0.2.5a7. I don't have it narrowed down to a small sample but can provide a bam with reads aligned against rice which is much smaller than human at least :)

[ edit ]

by this function I meant, I saw isBreakDancerEvent in my initial stack trace. I'm trying to track it further but valgrind is slooowww, probably take a week to show me anything

and I also can complete w/o using breakdancer input, but we see much better results with candidate site lists so...

[/edit]

it generally happens after looking at 10-20 mb of a chromosome, running each chr separately it would crash after last 'Looking' entry in the log.

Chr1. :Looking at chromosome Chr1 bases 1 to 5000001 of the bed region: chromosome Chr1:1-43270923
Chr1. :Looking at chromosome Chr1 bases 5000001 to 10000001 of the bed region: chromosome Chr1:1-43270923
Chr1. :Looking at chromosome Chr1 bases 10000001 to 15000001 of the bed region: chromosome Chr1:1-43270923
Chr1. :Looking at chromosome Chr1 bases 15000001 to 20000001 of the bed region: chromosome Chr1:1-43270923
Chr10. :Looking at chromosome Chr10 bases 1 to 5000001 of the bed region: chromosome Chr10:1-23207287
Chr10. :Looking at chromosome Chr10 bases 5000001 to 10000001 of the bed region: chromosome Chr10:1-23207287
Chr10. :Looking at chromosome Chr10 bases 10000001 to 15000001 of the bed region: chromosome Chr10:1-23207287
Chr11. :Looking at chromosome Chr11 bases 1 to 5000001 of the bed region: chromosome Chr11:1-29021106
Chr11. :Looking at chromosome Chr11 bases 5000001 to 10000001 of the bed region: chromosome Chr11:1-29021106
Chr12. :Looking at chromosome Chr12 bases 1 to 5000001 of the bed region: chromosome Chr12:1-27531856
Chr12. :Looking at chromosome Chr12 bases 5000001 to 10000001 of the bed region: chromosome Chr12:1-27531856
Chr12. :Looking at chromosome Chr12 bases 10000001 to 15000001 of the bed region: chromosome Chr12:1-27531856
Chr2. :Looking at chromosome Chr2 bases 1 to 5000001 of the bed region: chromosome Chr2:1-35937250
Chr2. :Looking at chromosome Chr2 bases 5000001 to 10000001 of the bed region: chromosome Chr2:1-35937250
Chr2. :Looking at chromosome Chr2 bases 10000001 to 15000001 of the bed region: chromosome Chr2:1-35937250
Chr2. :Looking at chromosome Chr2 bases 15000001 to 20000001 of the bed region: chromosome Chr2:1-35937250
Chr3. :Looking at chromosome Chr3 bases 1 to 5000001 of the bed region: chromosome Chr3:1-36413819
Chr3. :Looking at chromosome Chr3 bases 5000001 to 10000001 of the bed region: chromosome Chr3:1-36413819
Chr3. :Looking at chromosome Chr3 bases 10000001 to 15000001 of the bed region: chromosome Chr3:1-36413819
Chr4. :Looking at chromosome Chr4 bases 1 to 5000001 of the bed region: chromosome Chr4:1-35502694
Chr4. :Looking at chromosome Chr4 bases 5000001 to 10000001 of the bed region: chromosome Chr4:1-35502694
Chr4. :Looking at chromosome Chr4 bases 10000001 to 15000001 of the bed region: chromosome Chr4:1-35502694
Chr5. :Looking at chromosome Chr5 bases 1 to 5000001 of the bed region: chromosome Chr5:1-29958434
Chr5. :Looking at chromosome Chr5 bases 5000001 to 10000001 of the bed region: chromosome Chr5:1-29958434
Chr5. :Looking at chromosome Chr5 bases 10000001 to 15000001 of the bed region: chromosome Chr5:1-29958434
Chr5. :Looking at chromosome Chr5 bases 15000001 to 20000001 of the bed region: chromosome Chr5:1-29958434
Chr5. :Looking at chromosome Chr5 bases 20000001 to 25000001 of the bed region: chromosome Chr5:1-29958434
Chr5. :Looking at chromosome Chr5 bases 25000001 to 29958434 of the bed region: chromosome Chr5:1-29958434
Chr6. :Looking at chromosome Chr6 bases 1 to 5000001 of the bed region: chromosome Chr6:1-31248787
Chr6. :Looking at chromosome Chr6 bases 5000001 to 10000001 of the bed region: chromosome Chr6:1-31248787
Chr7. :Looking at chromosome Chr7 bases 1 to 5000001 of the bed region: chromosome Chr7:1-29697621
Chr7. :Looking at chromosome Chr7 bases 5000001 to 10000001 of the bed region: chromosome Chr7:1-29697621
Chr7. :Looking at chromosome Chr7 bases 10000001 to 15000001 of the bed region: chromosome Chr7:1-29697621
Chr7. :Looking at chromosome Chr7 bases 15000001 to 20000001 of the bed region: chromosome Chr7:1-29697621
Chr8. :Looking at chromosome Chr8 bases 1 to 5000001 of the bed region: chromosome Chr8:1-28443022
Chr8. :Looking at chromosome Chr8 bases 5000001 to 10000001 of the bed region: chromosome Chr8:1-28443022
Chr8. :Looking at chromosome Chr8 bases 10000001 to 15000001 of the bed region: chromosome Chr8:1-28443022
Chr8. :Looking at chromosome Chr8 bases 15000001 to 20000001 of the bed region: chromosome Chr8:1-28443022
Chr9. :Looking at chromosome Chr9 bases 1 to 5000001 of the bed region: chromosome Chr9:1-23012720
Chr9. :Looking at chromosome Chr9 bases 5000001 to 10000001 of the bed region: chromosome Chr9:1-23012720