kraken-build

[khuch123]

kraken-build --download-taxonomy --db HumanVirusBacteria bash: /bin/kraken-build: Permission denied and on perl kraken-build --download-taxonomy --db HumanVirusBacteria Can't exec "download_taxonomy.sh": Permission denied at kraken-build line 253

[khuch123]

Please reply at the earliest

[jenniferlu717]

Did you install kraken properly? (aka, run sh install_kraken.sh). It should make the command lines available for you to run as "kraken-build"

[khuch123]

Yes I did so I ran bash install_ kraken.sh kraken It wrote kraken installation complete Then it made certain scripts and files

Although I am able to run perl kraken-build command but then it comes cant exec download_taxonomy.sh

Changing the permissions also dont work

Please help

Regards

On Mon, 9 Apr 2018 at 11:14 PM, jenniferlu717 notifications@github.com wrote:

Did you install kraken properly? (aka, run sh install_kraken.sh). It should make the command lines available for you to run as "kraken-build"

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DerrickWood/kraken/issues/118#issuecomment-379835364, or mute the thread https://github.com/notifications/unsubscribe-auth/AjEH4P03GthTHw2e1LXWCg9p7Xz26Kd4ks5tm54agaJpZM4TMiu4 .

[khuch123]

Shall I provide you the line-by-line command that I executed so that you might have a better idea Or if there is something else that I can do to it

Regards Himani

On Tue, 10 Apr 2018 at 12:49 AM, HIMANI KHURANA himani.khurana1@gmail.com wrote:

Yes I did so I ran bash install_ kraken.sh kraken It wrote kraken installation complete Then it made certain scripts and files

Although I am able to run perl kraken-build command but then it comes cant exec download_taxonomy.sh

Changing the permissions also dont work

Please help

Regards

On Mon, 9 Apr 2018 at 11:14 PM, jenniferlu717 notifications@github.com wrote:

Did you install kraken properly? (aka, run sh install_kraken.sh). It should make the command lines available for you to run as "kraken-build"

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DerrickWood/kraken/issues/118#issuecomment-379835364, or mute the thread https://github.com/notifications/unsubscribe-auth/AjEH4P03GthTHw2e1LXWCg9p7Xz26Kd4ks5tm54agaJpZM4TMiu4 .

[your-highness]

Try

sudo chmod 755 /bin/kraken*

or

mkdir -p ~/bin/ 
cp /bin/kraken* ~/bin/kraken
chmod 755 ~/bin/kraken
export PATH=$PATH:~/bin/ 

[khuch123]

Okay Thank you

I will try and revert in a while.

On Tue, Apr 10, 2018 at 11:55 AM, Johannes Helmuth <notifications@github.com

wrote:

Try

sudo chmod 755 /bin/kraken*

or

mkdir -p ~/bin/ cp /bin/kraken* ~/bin/kraken chmod 755 ~/bin/krakenexport PATH=$PATH:~/bin/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DerrickWood/kraken/issues/118#issuecomment-379988030, or mute the thread https://github.com/notifications/unsubscribe-auth/AjEH4OR2ldDzm6FlD1uT4avNAGfRAFdJks5tnFBSgaJpZM4TMiu4 .

[khuch123]

/media/ruplal/Elements1/kraken/kraken_dir$ cp /bin/kraken* ~/bin/kraken cp: target ‘/home/ruplal/bin/kraken’ is not a directory

[khuch123]

bash: ./kraken-build: Permission denied

[khuch123]

Also the problem occurs while doing this on an external hard disk but on server it works fine but have space issues so used an external hard disk

[khuch123]

Hello I just wanted to tell you that I was able to install kraken It has been almost 24 hours that it is at step1 of kraken Creating k-mer set (step 1 of 6) Found jellyfish v1.1.10 Hash size not specified, using 18937420000

Although no error reported but is there anything wrong that I might be doing I have my server with 128 GB memory and 1TB space in hard disk It is already consuming around 107 GB I have also specified threads=20

Is there something else I should do?

Regards

[khuch123]

Please reply because I am struggling with this aspect since almost a week now

[khuch123]

Please reply Your response is awaited

[your-highness]

Seems the kraken-build binary does not have executable rights. Try chmod 755 kraken-build

[khuch123]

Please see the other issues posted I was able to run kraken-build However there is another issue Please help resolve that at the earliest

It has been almost 3 days that it is at step1 of kraken Creating k-mer set (step 1 of 6) Found jellyfish v1.1.10 Hash size not specified, using 18937420000

The path for database is in external hard disk

Although no error reported but is there anything wrong that I might be doing I have my server with 128 GB memory and 1TB space in hard disk It is already consuming around 107 GB I have also specified threads=20

Is there something else I should do?

On Mon, Apr 16, 2018 at 12:08 PM, Johannes Helmuth <notifications@github.com

wrote:

Seems the kraken-build binary does not have executable rights. Try chmod 755 kraken-build

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DerrickWood/kraken/issues/118#issuecomment-381494513, or mute the thread https://github.com/notifications/unsubscribe-auth/AjEH4ETfXhI43V2cDn7i281TzFJVtYIMks5tpDxugaJpZM4TMiu4 .

[jenniferlu717]

If you have human in your database along with bacteria and archaea, it might just be that your database is too big for your server size

[khuch123]

No it is just bacteria which is 37.1 Gb and a few Mb data of virus, archaea and plasmids.

Please suggest, should it be that I had to use work-on-disk switch for I am building that database in external hard disk?

Regards Himani

On Mon, Apr 16, 2018 at 12:37 PM, jenniferlu717 notifications@github.com wrote:

If you have human in your database along with bacteria and archaea, it might just be that your database is too big for your server size

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DerrickWood/kraken/issues/118#issuecomment-381500369, or mute the thread https://github.com/notifications/unsubscribe-auth/AjEH4OnEn_rRLeCsvznHBW85eYbYqHKvks5tpEMrgaJpZM4TMiu4 .

[khuch123]

Hello,

I used jellyfish hash size 6400 M and my server has only 125 Gb memory,it is stuck at step 3 since past two days, then what should be done?

Regards Himani

On Mon, Apr 16, 2018 at 12:50 PM, HIMANI KHURANA himani.khurana1@gmail.com wrote:

No it is just bacteria which is 37.1 Gb and a few Mb data of virus, archaea and plasmids.

Please suggest, should it be that I had to use work-on-disk switch for I am building that database in external hard disk?

Regards Himani

On Mon, Apr 16, 2018 at 12:37 PM, jenniferlu717 notifications@github.com wrote:

If you have human in your database along with bacteria and archaea, it might just be that your database is too big for your server size

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/DerrickWood/kraken/issues/118#issuecomment-381500369, or mute the thread https://github.com/notifications/unsubscribe-auth/AjEH4OnEn_rRLeCsvznHBW85eYbYqHKvks5tpEMrgaJpZM4TMiu4 .

[tingning-94]

Hi khuch123, i have stucked at the same issue as you. May I know did u manage to figure it out? If yes, do u mind to guide me? Thank you.