quickmerge aborted

[khush876]

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]

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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#64>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZQH2GO2AGGR7D6574TDCLTSZAZJANCNFSM46VW47IA> .

-- 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]

Thank you Mahul.

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

I do not see this information in the notes?

[mahulchak]

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? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#64 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZQH2CD7BXOAWHEIUCLBNDTSZFKBANCNFSM46VW47IA> .

-- 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]

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

[mahulchak]

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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#64 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZQH2F2UWZHJKOTVFXYDQDTSZGP3ANCNFSM46VW47IA> .

-- 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]

thanks

[khush876]

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]

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 <#64 (comment)>, 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