snp-eff download make error

[mcnaircm]

So everything has been working smoothly as far as alignment and variant calling up to this point, however, when I try to download the human snpeff database I get a make error. Here is the code:

gkno snpeff-download -d human [ 3:37PM]

University of Utah gkno package

version: 2.58.0 date: June 2016

git commit: ee73fde97ca0e649661ceec22f8d35d56880a0d1

Workflow: download (snpeff-download): Download SnpEff database.

Logging gkno usage with ID: snpeff-download...complete. Executing task: download...make: *\ [/home/cmm024/Tools_Installed/gkno_launcher/tools/snpEff/data/test] Error 255 make: Target `all' not remade because of errors.

I get this error no matter which data base I try to download... I'm not sure if its something that I need to fix on my end, but everything was working fine up until this!

-Chris

[AlistairNWard]

When you ran this, there should have been a file created called snpeff-download.XXX.stderr. Would you mind sending me the contents of this file? This should help diagnose the problem with the execution. My concern is something firewall related. Since you were not able to download resources, I'm guessing this is the same issue. Anyway, let me know what's in that file, and we'll try and diagnose.

Alistair Ward, PhD Director, Research and Science Department of Human Genetics USTAR Center for Genetic Discovery Eccles Institute of Human Genetics University of Utah School of Medicine​ 15 North 2030 East, Room 7140 Salt Lake City, UT 84112-5330

Co-founder, Frameshift labs, LLC

On Tue, Jun 28, 2016 at 3:43 PM, mcnaircm notifications@github.com wrote:

So everything has been working smoothly as far as alignment and variant calling up to this point, however, when I try to download the human snpeff database I get a make error. Here is the code:

gkno snpeff-download -d human [ 3:37PM]

University of Utah gkno package

version: 2.58.0 date: June 2016 git commit: ee73fde https://github.com/gkno/gkno_launcher/commit/ee73fde97ca0e649661ceec22f8d35d56880a0d1

Workflow: download (snpeff-download): Download SnpEff database.

Logging gkno usage with ID: snpeff-download...complete. Executing task: download...make: *** [/home/cmm024/Tools_Installed/gkno_launcher/tools/snpEff/data/test] Error 255 make: Target `all' not remade because of errors.

I get this error no matter which data base I try to download... I'm not sure if its something that I need to fix on my end, but everything was working fine up until this!

-Chris

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[mcnaircm]

Here is the contents of snpeff-download.stderr:

at ca.mcgill.mcb.pcingola.interval.Genome.(Genome.java:102) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:594) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:562) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:422) at ca.mcgill.mcb.pcingola.snpEffect.Config.(Config.java:107) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:265) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:79) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:71) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:883) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:128)

I tried to run it twice so there are two different .stderr files and both have the same contents. Anyway let me know what you think, and if you think that there would be a workaround if it is a firewall issue!

Cheers, Chris

[AlistairNWard]

Oh, sorry, I totally missed this. The error is in your command line. There is no database with the name 'human'. If you want the database associated with the human reference genome GRCh37, you need to download the database GRCh37.75. One reason I am concerned about you not getting resources is that I've tried to make command lines simpler by ensuring you don't need to know this information or need to specify commonly used parameters. This is achieved by using parameter sets. For example, type the command 'gkno snpeff-download -h' and you get the help information for the pipeline. Under the pipeline are listed a number of parameter sets. In this case, if you use the human parameter set 'gkno snpeff-download -ps human -h', you will see all the parameters that are set by using the 'human' parameter set. In this case, the only parameter is that --database is set to GRCh37.75. So try:

gkno snpeff-download -ps human

and you should get the resources you need. In most cases, the parameter sets will include files associated with a resource bundle, so you would have to download that with gkno add-resource . I'm slowly changing over 'human' resources to grch37 and grch38 so you can use the two most commonly used sets of files. Downloading the bundles will give you the fasta, bwa indexes etc. If you want to use files you already have, you can create your own personalised parameter sets so you don't have to retype things on the command line over and over. Let me know if you want to know more and I'm happy to help.

Let me know if this works.

Al

Alistair Ward, PhD Director, Research and Science Department of Human Genetics USTAR Center for Genetic Discovery Eccles Institute of Human Genetics University of Utah School of Medicine​ 15 North 2030 East, Room 7140 Salt Lake City, UT 84112-5330

Co-founder, Frameshift labs, LLC

On Wed, Jun 29, 2016 at 8:34 AM, mcnaircm notifications@github.com wrote:

Here is the contents of snpeff-download.stderr:

at ca.mcgill.mcb.pcingola.interval.Genome.(Genome.java:102) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:594) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:562) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:422) at ca.mcgill.mcb.pcingola.snpEffect.Config.(Config.java:107) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:265) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:79) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:71) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:883) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:128)

I tried to run it twice so there are two different .stderr files and both have the same contents. Anyway let me know what you think, and if you think that there would be a workaround if it is a firewall issue!

Cheers, Chris

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[mcnaircm]

Great that worked perfectly! So just to clarify as of now you can only download one package through gkno and that is for grch37.75, unless I used gkno add-resource for grch37 or 38?

[AlistairNWard]

No, you can download as many packages as you like. Using gkno add-resource will download resource bundles containing lots of files for those resources. So if you added the GRCh37 gkno resource, it would download the reference fasta, all the bwa index files so you can start aligning immediately etc. It doesn't have any snpEff files in it. But, if you type gkno update-light, this will update gkno to the latest version. The 'light' part means it updates only the configuration files that define tools and pipelines. 'gkno update' will also update all of the tools themselves which will take a lot longer and they don't usually have any updates. If you update, then type:

gkno snpeff-databases

This will create a file called snpEff_databases.txt, which contains a list of all the databases that can be downloaded for use with snpeff. You can then download any of these using:

gkno snpeff-download --database

If you want the GRCh38 database, you can use:

gkno snpeff-download -ps grch38

You have to do the update first though, since I just added the GRCh38 parameter set and databases pipeline. Hope this helps,

Al

Alistair Ward, PhD Director, Research and Science Department of Human Genetics USTAR Center for Genetic Discovery Eccles Institute of Human Genetics University of Utah School of Medicine​ 15 North 2030 East, Room 7140 Salt Lake City, UT 84112-5330

Co-founder, Frameshift labs, LLC

On Wed, Jun 29, 2016 at 3:31 PM, mcnaircm notifications@github.com wrote:

Great that worked perfectly! So just to clarify as of now you can only download one package through gkno and that is for grch37.75, unless I used gkno add-resource for grch37 or 38?

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[AlistairNWard]

Hey Chris,

Just wanted to check in to see if gkno is working for you and if you are finding it useful? If there are any things that you were hoping to achieve that it isn't really helping with? Feedback is always appreciated to help support the project!

Al

Alistair Ward, PhD Director, Research and Science Department of Human Genetics USTAR Center for Genetic Discovery Eccles Institute of Human Genetics University of Utah School of Medicine​ 15 North 2030 East, Room 7140 Salt Lake City, UT 84112-5330

Co-founder, Frameshift labs, LLC

On Wed, Jun 29, 2016 at 4:32 PM, Alistair Ward alistairnward@gmail.com wrote:

No, you can download as many packages as you like. Using gkno add-resource will download resource bundles containing lots of files for those resources. So if you added the GRCh37 gkno resource, it would download the reference fasta, all the bwa index files so you can start aligning immediately etc. It doesn't have any snpEff files in it. But, if you type gkno update-light, this will update gkno to the latest version. The 'light' part means it updates only the configuration files that define tools and pipelines. 'gkno update' will also update all of the tools themselves which will take a lot longer and they don't usually have any updates. If you update, then type:

gkno snpeff-databases

This will create a file called snpEff_databases.txt, which contains a list of all the databases that can be downloaded for use with snpeff. You can then download any of these using:

gkno snpeff-download --database

If you want the GRCh38 database, you can use:

gkno snpeff-download -ps grch38

You have to do the update first though, since I just added the GRCh38 parameter set and databases pipeline. Hope this helps,

Al

Alistair Ward, PhD Director, Research and Science Department of Human Genetics USTAR Center for Genetic Discovery Eccles Institute of Human Genetics University of Utah School of Medicine​ 15 North 2030 East, Room 7140 Salt Lake City, UT 84112-5330

Co-founder, Frameshift labs, LLC

On Wed, Jun 29, 2016 at 3:31 PM, mcnaircm notifications@github.com wrote:

Great that worked perfectly! So just to clarify as of now you can only download one package through gkno and that is for grch37.75, unless I used gkno add-resource for grch37 or 38?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/gkno/gkno_launcher/issues/69#issuecomment-229463192, or mute the thread https://github.com/notifications/unsubscribe/AAf7Z1q6kwQZyz_cfzdCxq0AvDAdQ2wGks5qQsgigaJpZM4JAddo .

[mcnaircm]

Hey Al, Sorry for the super delayed response, I had been working on some other projects and completely forgot to get back to you! Anyway, everything seemed to work find after working through some initial issues, as far as alignment is concerned. What would be helpful though would be multiple variant annotation tools (other than just snpeff). It might also be cool to have a variant caller comparison tool (similar to what you guys have in demo on iobio). Anyway, I'm sure both of those things are no easy task but figured I'd suggest them nonetheless! Thanks again for all the help thusfar!