cnv_all.prefix.txt and small.prefix.txt are empty

[CAShuangchao]

Hi, I would like to ask you about two small problems encountered when running svmu. Here's the script I used: **nucmer --mum -p out msu.Chr6.fa r498.Chr6.fa delta-filter -i 80 -1 out.delta > out.filter.delta

touch last_out.txt svmu out.filter.delta msu.Chr6.fa r498.Chr6.fa h last_out.txt nucm**

First, when I run this script, a table with many lines pops up on the screen, like this: ....... gap Chr6 26089884 26090751 Chr6 27448116 27448564 Chr6 0 26062264 Chr6 27418463 27418463 gap Chr6 26091006 26092210 Chr6 27448837 27455791 Chr6 26093201 26093205 Chr6 27456766 27456770 gap Chr6 26093200 26093201 Chr6 27456770 27456770 Chr6 0 24760893 Chr6 2667338 2667668 gap Chr6 26093698 26093698 Chr6 26207565 26207566 ....... What kind of information is this? Is it important?

Second, my cnv_all.out.txt and small.out.txt are empty, is this normal? Is it because I used the empty file last_out.txt? (This is what I learned from the answers you gave to others).

In order to facilitate you to help me answer more quickly, I have attached the above generated files. New Folder.zip

Thank you for your help Huangchao

[mahulchak]

Thanks Huangchao. I'll take a look.

On Fri, May 7, 2021, 08:32 CAShuangchao @.***> wrote:

Hi, I would like to ask you about two small problems encountered when running svmu. Here's the script I used: **nucmer --mum -p out msu.Chr6.fa r498.Chr6.fa delta-filter -i 80 -1 out.delta > out.filter.delta

touch last_out.txt svmu out.filter.delta msu.Chr6.fa r498.Chr6.fa h last_out.txt nucm**

First, when I run this script, a table with many lines pops up on the screen, like this: ....... gap Chr6 26089884 26090751 Chr6 27448116 27448564 Chr6 0 26062264 Chr6 27418463 27418463 gap Chr6 26091006 26092210 Chr6 27448837 27455791 Chr6 26093201 26093205 Chr6 27456766 27456770 gap Chr6 26093200 26093201 Chr6 27456770 27456770 Chr6 0 24760893 Chr6 2667338 2667668 gap Chr6 26093698 26093698 Chr6 26207565 26207566 ....... What kind of information is this? Is it important?

Second, my cnv_all.out.txt and small.out.txt are empty, is this normal? Is it because I used the empty file last_out.txt? (This is what I learned from the answers you gave to others).

In order to facilitate you to help me answer more quickly, I have attached the above generated files. New Folder.zip https://github.com/mahulchak/svmu/files/6442658/New.Folder.zip

Thank you for your help Huangchao

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[yuan102379]

Hi @mahulchak

I have met with similar problems that both cnv_all.out.txt and small.out.txt are empty.

My codes are listed as followed:

nucmer

nucmer --maxmatch --threads 20 --prefix sam2ref ../0.fasta/HiC_scaffold_1.fasta ../0.fasta/HiC_scaffold_2.fasta

lastz

lastz ../0.fasta/HiC_scaffold_1.fasta[multiple] ../0.fasta/HiC_scaffold_2.fasta[multiple] --chain --format=general:name1,strand1,start1,end1,name2,strand2,start2,end2 > sam_lastz.txt

svmu

svmu sam2ref.delta ../0.fasta/HiC_scaffold_1.fasta ../0.fasta/HiC_scaffold_2.fasta h sam_lastz.txt prefix

Is it normal for the empty cnv_all.out.txt and small.out.txt?

Could you provide some suggestions, please?

Thanks a lot for your help & have a nice day.

Yours,

Yuan

[mahulchak]

Hi Yuan, Can you try without the maxmatch option and see if it works?

On Thu, Aug 19, 2021 at 2:21 AM Yuan @.***> wrote:

Hi @mahulchak https://github.com/mahulchak

I have met with similar problems that both cnv_all.out.txt and small.out.txt are empty.

My codes are listed as followed:

nucmer

nucmer --maxmatch --threads 20 --prefix sam2ref ../0.fasta/HiC_scaffold_1.fasta ../0.fasta/HiC_scaffold_2.fasta

lastz

lastz ../0.fasta/HiC_scaffold_1.fasta[multiple] ../0.fasta/HiC_scaffold_2.fasta[multiple] --chain --format=general:name1,strand1,start1,end1,name2,strand2,start2,end2 > sam_lastz.txt

svmu

svmu sam2ref.delta ../0.fasta/HiC_scaffold_1.fasta ../0.fasta/HiC_scaffold_2.fasta h sam_lastz.txt prefix

Is it normal for the empty cnv_all.out.txt and small.out.txt?

Could you provide some suggestions, please?

Thanks a lot for your help & have a nice day.

Yours,

Yuan

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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

[haoyanioz]

hi @mahulchak I have met with similar problems that both sv.tmp.txt and small.tmp.txt are empty. My codes are listed as followed:

nucmer

nucmer --maxmatch -c 90 -l 40 -t 75 ref.fa query.fa --prefix=tmp delta-filter -m -i 90 -l 100 tmp.delta > tmp.filt.delta

svmu

svmu tmp.filt.delta ref.fa query.fa l lastz.txt tmp

I'm not sure why it happened. Could you give me some suggestions?

Any help would be highly appreciated.

Cheers, STAR

[KewinOgink]

Hey @mahulchak I have the same problem, when running svmu with an empty lastz file, and I did not use the maxmatch option with nucmer. I only get lines in my standard output like this

Chr01   21959   21962   Chr01   86351   86354
gap     Chr01   13092   21959   Chr01   86354   86354
Chr01   0       21962   Chr01   86351   86354
gap     Chr01   65125   76130   Chr01   129439  132614

cheers,

Kewin