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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' #17

Closed shameem356 closed 7 years ago

shameem356 commented 7 years ago

Hello ,

I am facing a problem related to 'std::out_of_range'.When I ran quickmerge first time it worked fine with the following command1.But when I change the reference and query( Command 2 : swapped query & reference ) it showing the error std::out_of_range error.I am using latest build.Please let me know how can I solve the issue.

command 1 nucmer -l 100 -prefix out New_CspixV2gen.fa 0x_spix.fa delta-filter -i 95 -r -q out.delta > out.rq.delta quickmerge -d out.rq.delta -r New_CspixV2gen.fa -q 10x_spix.fa -hco 5.0 -c 1.5 -l 1000000 -ml 6000

command 2 nucmer -l 100 -prefix out 10x_spix.faNew_CspixV2gen.fa delta-filter -i 95 -r -q out.delta > out.rq.delta quickmerge -d out.rq.delta -r 10x_spix.fa -q New_CspixV2gen.fa -hco 5.0 -c 1.5 -l 1000000 -ml 6000

mahulchak commented 7 years ago

Is this the exact command you have used?

On Wed, Feb 15, 2017, 07:28 shameem356 notifications@github.com wrote:

Hello ,

I am facing a problem related to 'std::out_of_range'.When I ran quickmerge first time it worked fine with the following command1.But when I change the reference and query( Command 2 : swapped query & reference ) it showing the error std::out_of_range error.I am using latest build.Please let me know how can I solve the issue.

command 1 nucmer -l 100 -prefix out New_CspixV2gen.fa 0x_spix.fa delta-filter -i 95 -r -q out.delta > out.rq.delta quickmerge -d out.rq.delta -r New_CspixV2gen.fa -q 10x_spix.fa -hco 5.0 -c 1.5 -l 1000000 -ml 6000

command 2 nucmer -l 100 -prefix out 10x_spix.faNew_CspixV2gen.fa delta-filter -i 95 -r -q out.delta > out.rq.delta quickmerge -d out.rq.delta -r 10x_spix.fa -q New_CspixV2gen.fa -hco 5.0 -c 1.5 -l 1000000 -ml 6000

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shameem356 commented 7 years ago

Yes, I used the exact command in both cases.

mahulchak commented 7 years ago

In the quickmerge command line -q comes before -r. If you reverse the sequence, you'll get that error.

On Wed, Feb 15, 2017 at 10:24 AM shameem356 notifications@github.com wrote:

Yes, I used the exact command in both cases.

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RxLoutre commented 7 years ago

Hi Mahul !

I've got the same error using this command :

quickmerge -d out.rq.delta -q '/media/loutre/SUZUKII/assembly/falcon/falcon_cleaned_p_ctg.fasta' -r '/media/loutre/SUZUKII/assembly/canu/1-cleaned_names_canu3_suzukii.fasta' -hco 5.0 -c 1.5 -l 2000000 -ml 50000

The problem was that I wasn't using the same files for nucmer command and quickmerge command.

I let this here in case some will be not carefull enough like me and wonder what they have made wrong

shameem356 commented 7 years ago

Hello @mahulchak ,

Its worked for me when I used -q before -r.Thank you so much for help.