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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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quickmerge aborted #64

Open khush876 opened 3 years ago

khush876 commented 3 years ago

Hi,

I am getting this error while running quickmerge

quickmerge -d out.rq.delta -q IPA.fasta -r hifi-hybrid.fasta -hco 5.0 -c 1.5 -l n -ml m -p prefix

0 quickmerge 1 -d 2 out.rq.delta 3 -q 4 IPA.fasta 5 -r 6 hifi-hybrid.fasta 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 n 13 -ml 14 m 15 -p 16 prefix terminate called after throwing an instance of 'std::invalid_argument' what(): stoi /var/spool/slurmd/job4117374/slurm_script: line 15: 53965 Aborted

How to solve this issue?

mahulchak commented 3 years ago

Hi, You need to provide actual numbers in place of 'm' and 'n' in the command.

On Mon, Jun 14, 2021 at 11:12 AM khush876 @.***> wrote:

Hi,

I am getting this error while running quickmerge

quickmerge -d out.rq.delta -q IPA.fasta -r hifi-hybrid.fasta -hco 5.0 -c 1.5 -l n -ml m -p prefix

0 quickmerge 1 -d 2 out.rq.delta 3 -q 4 IPA.fasta 5 -r 6 hifi-hybrid.fasta 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 n 13 -ml 14 m 15 -p 16 prefix terminate called after throwing an instance of 'std::invalid_argument' what(): stoi /var/spool/slurmd/job4117374/slurm_script: line 15: 53965 Aborted

How to solve this issue?

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khush876 commented 3 years ago

Thank you Mahul.

what is the default values for 'M' and 'N'

I do not see this information in the notes?

mahulchak commented 3 years ago

They are generally case specific. You could perhaps start with 1000000 for n and 5000 for m ?

On Mon, Jun 14, 2021 at 11:50 AM khush876 @.***> wrote:

Thank you Mahul.

what is the default values for 'M' and 'N'

I do not see this information in the notes?

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-- 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

khush876 commented 3 years ago

Thank you. I really appreciate it. Now I got it. -l and -ml are the options for the this.

mahulchak commented 3 years ago

that's correct

On Mon, Jun 14, 2021 at 12:00 PM khush876 @.***> wrote:

Thank you. I really appreciate it. Now I got it. -l and -ml are the options for the this.

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-- 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

khush876 commented 3 years ago

thanks

khush876 commented 3 years ago

Hi Mahul,

four files were generate after finishing the process.

aln_summary_prefix.tsv param_summary_prefix.txt anchor_summary_prefix.txt merged_prefix.fasta

However, I have an issue -

hifi-hybrid.fasta - before assembly - 11,626 fasta sequences

after quickmerge with IPA.fasta as a query

merged_prefix.fasta - 11,622 fasta sequences

Is it correct? Why two long read assembly gave me similar number of fasta sequences after quickmerge.

Please suggest

mahulchak commented 3 years ago

If some merging took place, the merged file should have fewer sequences.

On Thu, Jun 17, 2021 at 10:50 PM khush876 @.***> wrote:

Hi Mahul,

four files were generate after finishing the process.

aln_summary_prefix.tsv param_summary_prefix.txt anchor_summary_prefix.txt merged_prefix.fasta

However, I have an issue -

hifi-hybrid.fasta - before assembly - 11,626 fasta sequences

after quickmerge with IPA.fasta as a query

merged_prefix.fasta - 11,622 fasta sequences

Is it correct? Why two long read assembly gave me similar number of fasta sequences after quickmerge.

Please suggest

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/mahulchak/quickmerge/issues/64#issuecomment-863774533, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZQH2C3WSKZALLSOGPFWW3TTLM67ANCNFSM46VW47IA .

-- 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