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Crash if output directory does not exist / file is not writable #113

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h-2 opened this issue Jan 31, 2018 · 1 comment
Closed

Crash if output directory does not exist / file is not writable #113

h-2 opened this issue Jan 31, 2018 · 1 comment
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@h-2
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bug
Milestone
1.9.4

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@h-2
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h-2 commented Jan 31, 2018

via e-mail:

I was also getting core dumps when the folders for the output file does
not exist.

I just wanted to check whether this is now fixed in the repository
version, it looks it has not been fixed. Copied below is the output of
the terminal where i run the test.

(gdb) r searchp -q ./brine/data/brine1-r1.h4000.fastq.gz -i
./uniprot/uniprot_sprot.fasta.gz.lambda -o test/test.m8
Starting program: /home/uludagm/bin/lambda2 searchp -q
./brine/data/brine1-r1.h4000.fastq.gz -i
./uniprot/uniprot_sprot.fasta.gz.lambda -o test/test.m8
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
WARNING: This binary is not built in release mode and will be much
slower than it should be!
Detaching after fork from child process 15818.
WARNING: This binary is not built in release mode and will be much
slower than it should be!
LAMBDA - the Local Aligner for Massive Biological DatA
======================================================
Version 1.9.4

Reading index properties... done.
Detecting query alphabet... dna5 detected.
Checking memory requirements... met.
Loading Subj Sequences...[New Thread 0x7ffff7ff68c0 (LWP 15820)]
  done.
Loading Subj Ids...[Thread 0x7ffff7ff68c0 (LWP 15820) exited]
  done.
Loading Database Index...[New Thread 0x7ffff7ff68c0 (LWP 15833)]
[Thread 0x7ffff7ff68c0 (LWP 15833) exited]
  done.
Loading Query Sequences and Ids...translating...[New Thread
0x7fffd0e60700 (LWP 15876)]
[New Thread 0x7fffd065f700 (LWP 15877)]
[New Thread 0x7fffcfe5e700 (LWP 15878)]
[New Thread 0x7fffcf65d700 (LWP 15879)]
[New Thread 0x7fffcee5c700 (LWP 15880)]
[New Thread 0x7fffce65b700 (LWP 15881)]
[New Thread 0x7fffcde5a700 (LWP 15882)]
[New Thread 0x7fffcd659700 (LWP 15883)]
[New Thread 0x7fffcce58700 (LWP 15884)]
[New Thread 0x7fffcc657700 (LWP 15885)]
[New Thread 0x7fffcbe56700 (LWP 15886)]
[New Thread 0x7fffcb655700 (LWP 15887)]
[New Thread 0x7fffcae54700 (LWP 15888)]
[New Thread 0x7fffca653700 (LWP 15889)]
[New Thread 0x7fffc9e52700 (LWP 15890)]
  done.
Searching and extending hits on-line...progress:
0%  10%  20%  30%  40%  50%  60%  70%  80%  90%  100%

|
Thread 1 "lambda2" received signal SIGSEGV, Segmentation fault.
std::basic_streambuf<char, std::char_traits<char> >::epptr (this=0x0)
     at
/usr/src/debug/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/streambuf:535
535          epptr() const { return _M_out_end; }
(gdb) bt
#0  std::basic_streambuf<char, std::char_traits<char> >::epptr (this=0x0)
     at
/usr/src/debug/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/streambuf:535
#1  0x0000000000fd3155 in seqan::getChunk<seqan::Range<char*>, char,
std::char_traits<char> > (result=..., buf=...)
     at
/home/uludagm/lambda/include/seqan/include/seqan/stream/iter_stream.h:545
#2  0x00000000011daee5 in seqan::getChunk<seqan::Range<char*>,
seqan::VirtualStream<char, seqan::Tag<seqan::Output_>,
std::char_traits<char> >, seqan::Output_> (result=..., iter=...) at
/home/uludagm/lambda/include/seqan/include/seqan/stream/iter_stream.h:554
#3  0x000000000123495b in
seqan::write<seqan::Iter<seqan::VirtualStream<char,
seqan::Tag<seqan::Output_>, std::char_traits<char> >,
seqan::StreamIterator<seqan::Tag<seqan::Output_> > >, char, unsigned
long> (target=...,
     ptr=0x1c16a45 "K00235:73:HKTWCBBXX:3:1101:6572:1387
1:N:0:AGTCAAK00235:73:HKTWCBBXX:3:1101:6978:1387
1:N:0:AGTCAAK00235:73:HKTWCBBXX:3:1101:7283:1387
1:N:0:AGTCAAK00235:73:HKTWCBBXX:3:1101:7364:1387 1:N:0:AGTCAAK002"..., n=36)
     at
/home/uludagm/lambda/include/seqan/include/seqan/basic/basic_stream.h:943
#4  0x0000000001235363 in
seqan::write<seqan::Iter<seqan::VirtualStream<char,
seqan::Tag<seqan::Output_>, std::char_traits<char> >,
seqan::StreamIterator<seqan::Tag<seqan::Output_> > >,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment> > (target=..., cont=...)
     at
/home/uludagm/lambda/include/seqan/include/seqan/basic/basic_stream.h:1095
#5  0x00000000012eab69 in
seqan::_writeField<seqan::Iter<seqan::VirtualStream<char,
seqan::Tag<seqan::Output_>, std::char_traits<char> >,
seqan::StreamIterator<seqan::Tag<seqan::Output_> > >, seqan::Score<int,
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>,
seqan::ScoreSpecSelectable> >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment>, unsigned int,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::BlastMatch<seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >, unsigned int,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment>, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::String<unsigned int,
seqan::Alloc<void> > >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, unsigned int,
(seqan::BlastProgram)2, (seqan::BlastTabularSpec)0> (s=..., context=...,
match=...,
     record=..., fieldId=seqan::BlastMatchField<void>::Enum::Q_SEQ_ID)
     at
/home/uludagm/lambda/include/seqan/include/seqan/blast/blast_tabular_out.h:266
#6  0x000000000128eff8 in
seqan::_writeMatch<seqan::Segment<seqan::String<char, seqan::Alloc<void>

 >, seqan::InfixSegment>, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Iter<seqan::VirtualStream<char, seqan::Tag<seqan::Output_>,
std::char_traits<char> >,
seqan::StreamIterator<seqan::Tag<seqan::Output_> > >, seqan::Score<int,
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>,
seqan::ScoreSpecSelectable> >, unsigned int,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::BlastMatch<seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >, unsigned int,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment>, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::String<unsigned int,
seqan::Alloc<void> > >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, unsigned int,
(seqan::BlastProgram)2, (seqan::BlastTabularSpec)0> (stream=...,
context=..., match=...,
     record=...) at
/home/uludagm/lambda/include/seqan/include/seqan/blast/blast_tabular_out.h:547
#7  0x000000000124f667 in
seqan::writeRecord<seqan::Iter<seqan::VirtualStream<char,
seqan::Tag<seqan::Output_>, std::char_traits<char> >,
seqan::StreamIterator<seqan::Tag<seqan::Output_> > >, seqan::Score<int,
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>,
seqan::ScoreSpecSelectable> >,
seqan::BlastMatch<seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >, unsigned int,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment>, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::String<unsigned int,
seqan::Alloc<void> > >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, unsigned int,
(seqan::BlastProgram)2, (seqan::BlastTabularSpec)0> (stream=...,
context=..., r=...)
---Type <return> to continue, or q <return> to quit---
    .h:654
#8  0x0000000001200abe in
seqan::writeRecord<seqan::BlastIOContext<seqan::Score<int,
seqan::ScoreMatrix<seqan::SimpleType<unsigned char, seqan::AminoAcid_>,
seqan::ScoreSpecSelectable> >, (seqan::BlastProgram)2,
(seqan::BlastTabularSpec)0>,
seqan::BlastMatch<seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >, unsigned int,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment>, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::String<unsigned int,
seqan::Alloc<void> > >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, unsigned int>
(formattedFile=..., r=...)
     at
/home/uludagm/lambda/include/seqan/include/seqan/blast/blast_tabular_out.h:664
#9  0x00000000011b0091 in
myWriteRecord<LocalDataHolder<GlobalDataHolder<seqan::SimpleType<unsigned
char, seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >,
seqan::FMIndex<void, LambdaFMIndexConfig>,
seqan::Tag<seqan::BlastTabular_>, (seqan::BlastProgram)2,
(seqan::BlastTabularSpec)0>, seqan::Tag<seqan::AffineGaps_> >,
seqan::BlastRecord<seqan::BlastMatch<seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >, unsigned int,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment>, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::String<unsigned int,
seqan::Alloc<void> > >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, unsigned int> > (lH=...,
record=...) at /home/uludagm/lambda/src/search_output.hpp:442
#10 0x00000000011486c4 in
_writeRecord<seqan::BlastRecord<seqan::BlastMatch<seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >,
seqan::Gaps<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::AminoAcid_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Tag<seqan::ArrayGaps_> >, unsigned int,
seqan::Segment<seqan::String<char, seqan::Alloc<void> >,
seqan::InfixSegment>, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::String<unsigned int,
seqan::Alloc<void> > >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, std::vector<std::string,
std::allocator<std::string> >, seqan::Segment<seqan::String<char,
seqan::Alloc<void> >, seqan::InfixSegment>, unsigned int>,
LocalDataHolder<GlobalDataHolder<seqan::SimpleType<unsigned char,
seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >,
seqan::FMIndex<void, LambdaFMIndexConfig>,
seqan::Tag<seqan::BlastTabular_>, (seqan::BlastProgram)2,
(seqan::BlastTabularSpec)0>, seqan::Tag<seqan::AffineGaps_> > >
(record=..., lH=...) at /home/uludagm/lambda/src/search_algo.hpp:1406
#11 0x00000000010c0a92 in
iterateMatchesFullSimd<LocalDataHolder<GlobalDataHolder<seqan::SimpleType<unsigned
char, seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >,
seqan::FMIndex<void, LambdaFMIndexConfig>,
seqan::Tag<seqan::BlastTabular_>, (seqan::BlastProgram)2,
(seqan::BlastTabularSpec)0>, seqan::Tag<seqan::AffineGaps_> > > (lH=...)
at /home/uludagm/lambda/src/search_algo.hpp:2518
#12 0x00000000010440d2 in
iterateMatches<LocalDataHolder<GlobalDataHolder<seqan::SimpleType<unsigned
char, seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >,
seqan::FMIndex<void, LambdaFMIndexConfig>,
seqan::Tag<seqan::BlastTabular_>, (seqan::BlastProgram)2,
(seqan::BlastTabularSpec)0>, seqan::Tag<seqan::AffineGaps_> > > (lH=...)
at /home/uludagm/lambda/src/search_algo.hpp:2653
#13 0x0000000000f63598 in realMain<seqan::FMIndex<void,
LambdaFMIndexConfig>, seqan::SimpleType<unsigned char,
seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >,
seqan::Tag<seqan::AffineGaps_>, seqan::Tag<seqan::BlastTabular_>,
(seqan::BlastProgram)2, (seqan::BlastTabularSpec)0> (
     options=...) at /home/uludagm/lambda/src/search.hpp:564
#14 0x0000000000000000 in ?? ()
(gdb)
@h-2 h-2 added the bug label Jan 31, 2018
@h-2 h-2 added this to the 1.9.4 milestone Jan 31, 2018
@h-2 h-2 self-assigned this Jan 31, 2018
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h-2 commented Jan 31, 2018

Should be fixed by 9ee1fb4

@h-2 h-2 closed this as completed Jan 31, 2018
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