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mahulchak / quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
GNU General Public License v3.0
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BUG for int type range #33

Open zhk2017 opened 5 years ago

zhk2017 commented 5 years ago

Because int type range is ( -2147483648 to 2147483647), when the merged genome size is over 2147483647 (2.15Gb) will report throw an error like "std::out_of_range".

From BerryGenomics zhk.

esolares commented 5 years ago

Hi

Are you using the 64bit version of mummer that was compiled with quickmerge?

Also can you please copy and paste the command that gave you this exception?

Thank you,

Edwin Solares

On Sun, Sep 9, 2018, 6:49 PM zhk2017 notifications@github.com wrote:

Because int type range is ( -2147483648 to 2147483647), when the merged genome size is over 2147483647 (2.15Gb) will report throw an error like "std::out_of_range".

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zhk2017 commented 5 years ago

The MUMmer is 64 bit, at the same time compile it use "make CPPFLAGS="-O3 -DSIXTYFOURBITS"".

Command is : python merge_wrapper.py -hco 5.0 -c 1.5 -l 190000 -lm 5000 method1.fa method2.fa

Error is: 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "out.ntref" of length 1856375413

construct suffix tree for sequence of length 1856375413

(maximum reference length is 2305843009213693948)

(maximum query length is 18446744073709551615)

process 18563754 characters per dot

....................................................................................................

CONSTRUCTIONTIME quickmerge/MUMmer3.23/mummer out.ntref 1201.77

reading input file "quick_merge_zhk/new/hybrid_oneline.fa" of length 2007539477

matching query-file "quick_merge_zhk/new/hybrid_oneline.fa"

against subject-file "out.ntref"

COMPLETETIME quickmerge/MUMmer3.23/mummer out.ntref 3677.68

SPACE quickmerge/MUMmer3.23/mummer out.ntref 3714.58

4: FINISHING DATA terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 18446744073709532943) > this->size() (which is 183703)

mahulchak commented 5 years ago

That's a strange error. I have not seen that error with MUMmer 3.x :|

On Sun, Sep 9, 2018, 19:15 zhk2017 notifications@github.com wrote:

The MUMmer is 64 bit, at the same time compile it use "make CPPFLAGS="-O3 -DSIXTYFOURBITS"".

Command is : python merge_wrapper.py -hco 5.0 -c 1.5 -l 190000 -lm 5000 method1.fa method2.fa

Error is: 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS reading input file "out.ntref" of length 1856375413 construct suffix tree for sequence of length 1856375413 (maximum reference length is 2305843009213693948) (maximum query length is 18446744073709551615) process 18563754 characters per dot

....................................................................................................

CONSTRUCTIONTIME /share/work4/chaijc/software/quickmerge/MUMmer3.23/mummer out.ntref 1201.77 reading input file "/share/science/Denovo/PBFC2017544/assembly_jiace/Sequel/quick_merge_zhk/new/hybrid_oneline.fa" of length 2007539477 matching query-file "/share/science/Denovo/PBFC2017544/assembly_jiace/Sequel/quick_merge_zhk/new/hybrid_oneline.fa" against subject-file "out.ntref" COMPLETETIME /share/work4/chaijc/software/quickmerge/MUMmer3.23/mummer out.ntref 3677.68 SPACE /share/work4/chaijc/software/quickmerge/MUMmer3.23/mummer out.ntref 3714.58

4: FINISHING DATA terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 18446744073709532943) > this->size() (which is 183703)

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