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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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terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 1047464) > this->size() (which is 0) Aborted #41

Open nrayamaj opened 5 years ago

nrayamaj commented 5 years ago

Hi,

When I try to run quickmerge using assembly A as reference (Illumina assembly ~746MB) and assembly B (nanopore assembly ~846MB) as query, it works fine.

However, when I switch assembly A as query and assembly B as reference, it throws an error: terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 1047464) > this->size() (which is 0) Aborted

I changed the file format (before running the quickmerge) using the following command in the both of cases: merge_wrapper.py nanopore_assembly.fasta illumina_assembly.fasta --no_nucmer --no_delta --clean_only

Could you please give me insight on this issue?

Regards, Niraj

nrayamaj commented 5 years ago

Please disregard the previous message.

Here is the problem: When I try to run quickmerge using assembly A as reference (nanopore assembly ~846MB) and assembly B (illumina assembly ~746MB) as query, it works fine.

However, when I switch assembly A as query and assembly B as reference, it throws an error: terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 1047464) > this->size() (which is 0) Aborted

I changed the file format (before running the quickmerge) using the following command in the both of cases: merge_wrapper.py nanopore_assembly.fasta illumina_assembly.fasta --no_nucmer --no_delta --clean_only

Could you please give me insight on this issue?

Regards, Niraj

ViriatoII commented 4 years ago

What is your N50? Is it possible that very big scaffolds as input create problems?

esolares commented 4 years ago

Again, we do not recommend using scaffolded assemblies on quickmerge.

With respect to n50's of contig assemblies. I have run quickmerge on 13Mb N50's and I believe Mahul has run it on assemblies with N50's much larger than that.

Thank you,

Edwin Solares, M.S. PhD Candidate in Comparative Genomics and Evolutionary Biology Department of Ecology and Evolutionary Biology Gaut Lab 5438 McGaugh Hall University of California, Irvine Irvine, CA 92697 USA

On Tue, Aug 6, 2019 at 7:49 AM ViriatoII notifications@github.com wrote:

What is your N50? Is it possible that very big scaffolds as input create problems?

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linshengnan2020 commented 3 years ago

hi，I also met this question: terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 82266) > this->size() (which is 0) ./work.sh: line 29: 352815 Aborted (core dumped) quickmerge -d next_mecat.out.rq.delta -q next_asm_awk1.fasta -r mecat2_asm_awk1.fasta -hco 5.0 -c 1.5 -l 249141 -ml 6000 -p next_mecat could you please give me some advises ? Thank you very much !

yangxiaofeill commented 2 years ago

I also have this problem.

terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr: __pos (which is 37148740) > this->size() (which is 0)

The contig N50 is larger, about 80Mb. How to address this problem?

mahulchak commented 2 years ago

do the sequence names have white space in them?

On Fri, Oct 22, 2021 at 5:24 AM yangxiaofeill @.***> wrote:

I also have this problem.

terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 37148740) > this->size() (which is 0)

The contig N50 is larger, about 80Mb. How to address this problem?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mahulchak/quickmerge/issues/41#issuecomment-949581607, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZQH2EXECTQVEILBP24YKTUIFJU5ANCNFSM4HZYL6IQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Mahul Chakraborty Department of Ecology and Evolutionary Biology University of California-Irvine Phone: 949 824 9559 Fax: 949 824 9559 Website: https://mahulchakraborty.wordpress.com/ Github: https://github.com/mahulchak