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vg index segmantation fault #674
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What is the maximum node size in the graph?
…On Thu, Feb 16, 2017, 8:46 PM shilpagarg ***@***.***> wrote:
I am doing vg index -x SK1+Y12.bwa.xg -g SK1+Y12.bwa.gcsa -k 16 SK1+
Y12.bwa.vg
and here is bt of segmentation fault:
#0 0x00000000009945c3 in std::pair<sdsl::wt_pc<sdsl::balanced_shape,
sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v<(unsigned char)1,
(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned
char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1>,
sdsl::byte_tree >::value_type, sdsl::wt_pc<sdsl::balanced_shape,
sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v<(unsigned char)1,
(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned
char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1>,
sdsl::byte_tree >::size_type>
sdsl::quantile_freq<sdsl::wt_pc<sdsl::balanced_shape,
sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v<(unsigned char)1,
(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned
char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1>,
sdsl::byte_tree > >(sdsl::wt_pc<sdsl::balanced_shape,
sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v<(unsigned char)1,
(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned
char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1>,
sdsl::byte_tree > const&, sdsl::wt_pc<sdsl::balanced_shape,
sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v<(unsigned char)1,
(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned
char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1>,
sdsl::byte_tree >::size_type, sdsl::wt_pc<sdsl::balanced_shape,
sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v<(unsigned char)1,
(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned
char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1>,
sdsl::byte_tree >::size_type, sdsl::wt_pc<sdsl::balanced_shape,
sdsl::int_vector<(unsigned char)1>, sdsl::rank_support_v<(unsigned char)1,
(unsigned char)1>, sdsl::select_support_mcl<(unsigned char)1, (unsigned
char)1>, sdsl::select_support_mcl<(unsigned char)0, (unsigned char)1>,
sdsl::byte_tree >::size_type) ()
#1 <#1> 0x00000000009861e5 in
gcsa::LCP::min_lcp(gcsa::PathNode const&, gcsa::PathNode const&, unsigned
int const*, unsigned int const*) const ()
#2 <#2> 0x0000000000986611 in
gcsa::PathRange::PathRange(unsigned long, unsigned long, std::pair<unsigned
long, unsigned long>, gcsa::PathGraphMerger&) ()
#3 <#3> 0x000000000098e48c in
gcsa::PathGraphMerger::next() ()
#4 <#4> 0x000000000098fd0e in
gcsa::PathGraph::prune(gcsa::LCP const&, unsigned long) ()
#5 <#5> 0x0000000000950da3 in
gcsa::GCSA::GCSA(gcsa::InputGraph&, gcsa::ConstructionParameters const&) ()
#6 <#6> 0x000000000069a214 in
main_index(int, char**) () at src/subcommand/index_main.cpp:873
#7 <#7> 0x00000000004182f2 in main ()
at src/main.cpp:7676
Here is the graph:
https://transfer.sh/YP4fM/sk1-y12.bwa.vg
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You may have run out of memory or disk space. The third doubling step creates a graph with 2.5 billion nodes and uses over 140 gigabytes of memory. The final graph is 10x smaller, and the order-128 index takes a little under a gigabyte. If you use only two doubling steps, you get a much more reasonable index. |
I chopped graph using vg mod -X 64 SK1+Y12.bwa.vg > SK1+Y12.bwa_X.vg and then index it using vg run index -x SK1+Y12.bwa.xg -g SK1+Y12.bwa.gcsa -k 8 -X 2 SK1+Y12.bwa.vg and I get
|
You're not passing SK1+Y12.bwa_X.vg to your index command in that
example...
…On Fri, Feb 17, 2017 at 1:23 PM, shilpagarg ***@***.***> wrote:
I chopped graph using
vg mod -X 64 SK1+Y12.bwa.vg > SK1+Y12.bwa_X.vg
and then index it using
vg run index -x SK1+Y12.bwa.xg -g SK1+Y12.bwa.gcsa -k 8 -X 2 SK1+
Y12.bwa.vg
and I get
#0 0x000000000098de6d in gcsa::PathGraphMerger::read(gcsa::PriorityNode&) ()
#1 0x000000000098e04c in gcsa::PathGraphMerger::bufferNext() ()
#2 0x000000000098e295 in gcsa::PathGraphMerger::rangeEnd(unsigned long) ()
#3 0x000000000098e622 in gcsa::PathGraphMerger::first() ()
#4 0x000000000098f7f8 in gcsa::PathGraph::prune(gcsa::LCP const&, unsigned long) ()
#5 0x0000000000950da3 in gcsa::GCSA::GCSA(gcsa::InputGraph&, gcsa::ConstructionParameters const&) ()
#6 0x000000000069a214 in main_index(int, char**) () at src/subcommand/index_main.cpp:873
#7 0x00000000004182f2 in main () at src/main.cpp:7676
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sorry I copied the wrong command, but I ran the right one. vg index -x SK1+Y12.bwa_X.xg -g SK1+Y12.bwa_X.gcsa -k 8 -X 2 SK1+Y12.bwa_X.vg That is why the backtrace now is different than the previous one. |
I face the same issue for chrI as well and here is the chopped vg graph: https://transfer.sh/nA8LE/sk1-y12.bwa-x.chri.vg and backtrace
|
Using the latest vg, I just ran
wget https://transfer.sh/nA8LE/sk1-y12.bwa-x.chri.vg
vg index -x SK1+Y12.bwa_X.xg -g SK1+Y12.bwa_X.gcsa -k 8 -X 2
sk1-y12.bwa-x.chri.vg
without any crash or error message. Took about 2min on 8 cores and 2G RAM.
ls -l
…-rw-rw-r-- 1 hickey hickey 6557138 Feb 17 15:54 sk1-y12.bwa-x.chri.vg
-rw-rw-r-- 1 hickey hickey 26977467 Feb 17 15:56 SK1+Y12.bwa_X.gcsa
-rw-rw-r-- 1 hickey hickey 14710097 Feb 17 15:56 SK1+Y12.bwa_X.gcsa.lcp
-rw-rw-r-- 1 hickey hickey 21853206 Feb 17 15:55 SK1+Y12.bwa_X.xg
On Fri, Feb 17, 2017 at 2:43 PM, shilpagarg ***@***.***> wrote:
I face the same issue for chrI as well and here is the chopped vg graph:
https://transfer.sh/nA8LE/sk1-y12.bwa-x.chri.vg
and backtrace
#0 0x000000000098de6d in gcsa::PathGraphMerger::read(gcsa::PriorityNode&) ()
#1 0x000000000098e04c in gcsa::PathGraphMerger::bufferNext() ()
#2 0x000000000098e295 in gcsa::PathGraphMerger::rangeEnd(unsigned long) ()
#3 0x000000000098e622 in gcsa::PathGraphMerger::first() ()
#4 0x000000000098f7f8 in gcsa::PathGraph::prune(gcsa::LCP const&, unsigned long) ()
#5 0x0000000000950da3 in gcsa::GCSA::GCSA(gcsa::InputGraph&, gcsa::ConstructionParameters const&) ()
#6 0x000000000069a214 in main_index(int, char**) () at src/subcommand/index_main.cpp:873
#7 0x00000000004182f2 in main () at src/main.cpp:7676
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I am doing vg index -x SK1+Y12.bwa.xg -g SK1+Y12.bwa.gcsa -k 16 SK1+Y12.bwa.vg
and here is bt of segmentation fault:
Here is the graph:
https://transfer.sh/YP4fM/sk1-y12.bwa.vg
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