Error report with sample data

[linzhi2013]

Error report with sample data

[linzhi2013]

Hi

This was most likely caused by there was not enough memory available. 1. How much data did you provide to mitoz? 2. How much memory does your server have?

[srimku]

it has 16 GB ram 5 TB hard disk

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On Tue, Jan 28, 2020 at 3:34 PM Guanliang MENG ***@***.***> wrote: Hi This was most likely caused by there was not enough memory available. 1. How much data did you provide to mitoz? 2. How much memory does your server have? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AOKXR576ZZDY4BZW675FNRDQ777JLA5CNFSM4KMN6S32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKCWXZI#issuecomment-579169253>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOKXR52OAFSCA3IYUBO6R2LQ777JLANCNFSM4KMN6S3Q> .

-- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: [phone] Fax: [phone] Mobile: [phone] Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* ***************************************************

[srimku]

Is it possible to run mitoZ with this memory? Please give your suggestions to run mitoz for my data

…

On Tue, Jan 28, 2020 at 3:40 PM Sridhar j ***@***.***> wrote: it has 16 GB ram 5 TB hard disk On Tue, Jan 28, 2020 at 3:34 PM Guanliang MENG ***@***.***> wrote: > Hi > > This was most likely caused by there was not enough memory available. 1. > How much data did you provide to mitoz? 2. How much memory does your server > have? > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#45?email_source=notifications&email_token=AOKXR576ZZDY4BZW675FNRDQ777JLA5CNFSM4KMN6S32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKCWXZI#issuecomment-579169253>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AOKXR52OAFSCA3IYUBO6R2LQ777JLANCNFSM4KMN6S3Q> > . > -- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: [phone] Fax: [phone] Mobile: [phone] Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* ***************************************************

-- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: [phone] Fax: [phone] Mobile: [phone] Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* ***************************************************

[linzhi2013]

Hi

16G RAM is generously not enough, unless the input data is very small, for example, the test data in this GitHub project. If the input data is ca. 2Gb, you need about 60G ram at least. You may check the readme file for more details.

Thanks!

[srimku]

Dear Dr. Meng, I dont have access to the workstation with 64 G RAM. Is their any possibility of providing workstation support to run for my input files (2 Gb in size). Please help me to make a run for my data. Thank you sincerely Sridhar

…

On Tue, Jan 28, 2020 at 3:52 PM Guanliang MENG ***@***.***> wrote: Hi 16G RAM is generously not enough, unless the input data is very small, for example, the test data in this GitHub project. If the input data is ca. 2Gb, you need about 60G ram at least. You may check the readme file for more details. Thanks! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AOKXR5Z4B2URBL3I4IADFADRAABNBA5CNFSM4KMN6S32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKCYSDI#issuecomment-579176717>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOKXR5YSYMKBMCJZK2GKHCDRAABNBANCNFSM4KMN6S3Q> .

-- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: [phone] Fax: [phone] Mobile: [phone] Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* ***************************************************

[linzhi2013]

Hi Sridhar,

You may check out the 2.3 Memory on https://github.com/linzhi2013/MitoZ/

Hope this helps.

Cheers
Guanliang

[srimku]

Sorry, I am not getting this usage with less memory. Can you explain it how could i use MitoZ with less memory (16 G RAM).

…

On Mon, Feb 24, 2020 at 5:36 PM Guanliang MENG ***@***.***> wrote: Hi Sridhar, You may check out the *2.3 Memory* on https://github.com/linzhi2013/MitoZ/ Hope this helps. Cheers Guanliang — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AOKXR5YFI2NM5UNQINPSPODREOZ4NA5CNFSM4KMN6S32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMXRVGQ#issuecomment-590289562>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOKXR52NXJSCPMLCLTJ4GNDREOZ4NANCNFSM4KMN6S3Q> .

-- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: [phone] Fax: [phone] Mobile: [phone] Web:*http://www.genomicsmku.org/FAC%20PROF/srithar.html <http://www.genomicsmku.org/FAC%20PROF/srithar.html>* ***************************************************

[linzhi2013]

Sorry, I am not getting this usage with less memory. Can you explain it how could i use MitoZ with less memory (16 G RAM).
…
On Mon, Feb 24, 2020 at 5:36 PM Guanliang MENG @.***> wrote: Hi Sridhar, You may check out the 2.3 Memory on https://github.com/linzhi2013/MitoZ/ Hope this helps. Cheers Guanliang — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#45?email_source=notifications&email_token=AOKXR5YFI2NM5UNQINPSPODREOZ4NA5CNFSM4KMN6S32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMXRVGQ#issuecomment-590289562>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOKXR52NXJSCPMLCLTJ4GNDREOZ4NANCNFSM4KMN6S3Q .
-- *************************************************** Dr. Jayavel Sridhar UGC-Commonwealth Doctoral Fellow-UK Assistant Professor Department of Biotechnology (DDE) Madurai Kamaraj University (University with Potential for Excellence) Madurai-625021 INDIA Phone: [phone] Fax: [phone] Mobile: [phone] Web:http://www.genomicsmku.org/FAC%20PROF/srithar.html http://www.genomicsmku.org/FAC%20PROF/srithar.html ***************************************************

You can use BWA (https://github.com/lh3/bwa) to align your fastq reads again some closely related species (with relaxed parameters) and then extracted only the mapped reads with samtools (https://github.com/samtools/) output in fastq format.

then using the result fastq reads for mitogenome assembly.

now this method has been updated on https://github.com/linzhi2013/MitoZ/blob/master/version_2.4-alpha/README.md.