I would like to use Drosophila melanogaster : BDGP5.74. I did the two steps you suggested to me to install the annotation. I also did from command line. But, there is no the option of BDGP5.74 from the "Genome" drop-down menu in SnpEff. The version of
SnpEff is version 1.0 and I used SnpEfff in CloudMap workflow. Do you know why and how to figure it out? (In fact, it works fine for BDGP5.66.)
Xiaofei
________________________________________
From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfwang@ku.edu]
Sent: Thursday, April 03, 2014 3:52 PM
To: Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Oh, hooray, I figured it out.
what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again:
java -jar snpEff.jar download dm5.42
Thank you so much!
Best,
Xiaofei
_____________________________________
From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfwang@ku.edu]
Sent: Thursday, April 03, 2014 10:31 AM
To: Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>1. click "SnpEff Download"
>2. choose one genome from "SnpEff Databases" and install it
Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is:
java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'.
You can try to download the database by running the following command:
java -jar snpEff.jar download dm5.42
at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58)
at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem?
May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed
data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times):
Data Manager: snpeff_genomedb
value name path
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
________________________________________
From: Björn Grüning [bjoern.gruening@gmail.com]
Sent: Thursday, April 03, 2014 5:25 AM
To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
>> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.
It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.
1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install it
> Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response.
> But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?
Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?
Cheers,
Bjoern
> When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?
>
> Thank you so much!
>
> Best,
>
> Xiaofei
>
> ________________________________________
> From: Björn Grüning [bjoern.gruening@gmail.com]
> Sent: Wednesday, April 02, 2014 4:17 PM
> To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear Bjoern,
>> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
>> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
>> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
>> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.
>
> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> Hope that will help!
> Bjoern
>
>>
>> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>>
>> I really appreciate for your help, and thank you so much for your patience!
>>
>> Best,
>>
>> Xiaofei
>> Data Manager
>>
>> Choose your data managing option from below.
>>
>> * Access data managers - get data, build indexes, etc
>>
>> * SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by manager
>>
>> * SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by Tool Data Table
>>
>> * snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>>
>> * snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>>
>> * snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>>
>> * snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>>
>> * bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>>
>> * bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>>
>> * all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>> *
>> *
>> *
>> * ________________________________________
>> * From: Björn Grüning [bjoern.gruening@gmail.com]
>> * Sent: Wednesday, April 02, 2014 12:55 PM
>> * To: Wang, Xiaofei; Björn Grüning; galaxy-dev@lists.bx.psu.edu
>> * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> *
>> * Hi,
>> *
>> * that means that the snpeff annotation is missing. You can install it
>> * with the snpeff datamanager under your Admin panel. Have a look at the
>> * wiki page about data-manager and the snpeff wrapper documentation.
>> * You do not need to edit xml files. If so that is an bug in the wrapper
>> * and we should fix it :)
>> *
>> * Cheers,
>> * Bjoern
>> *
>> * Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>> * >>> When I used SnpEff in local galaxy instance, I got an error:
>> * >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * >
>> * >
>> * >
>> * >> Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >
>> * >
>> * >
>> * > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>> * >
>> * >
>> * >
>> * >
>> * > But, I got another error for snpEff.
>> * >
>> * >
>> * >
>> * >
>> * > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>> * > at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>> * >
>> * >
>> * >
>> * >
>> * > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down
menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>> * >
>> * >
>> * >
>> * >
>> * > <param name="genomeVersion" type="select" label="Genome">
>> * > <option value="hg37">Human (hg37)<option>
>> * > <option value="mm37.61">Mouse (mm37.61)<option>
>> * > <param>
>> * >
>> * >
>> * >
>> * > ________________________________________
>> * > From: Björn Grüning [bjoern.gruening@gmail.com]
>> * > Sent: Wednesday, April 02, 2014 10:35 AM
>> * > To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
>> * > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> * >
>> * > Hi Xiaofei,
>> * >
>> * >> Dear there,
>> * >>
>> * >> When I used SnpEff in local galaxy instance, I got an error:
>> * >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * > Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> * >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>> * >
>> * > Can you give us the complete error message. The important part is missing.
>> * >
>> * > Ciao,
>> * > Bjoern
>> * >
>> * >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>> * >>
>> * >>
>> * >>
>> * >>
>> * >> ___________________________________________________________
>> * >> Please keep all replies on the list by using "reply all"
>> * >> in your mail client. To manage your subscriptions to this
>> * >> and other Galaxy lists, please use the interface at:
>> * >> http://lists.bx.psu.edu/
>> * >>
>> * >> To search Galaxy mailing lists use the unified search at:
>> * >> http://galaxyproject.org/search/mailinglists/
>> * >>
>> * >
>> * >
>> *
>> *
>>
>
>
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___________________________________________________________
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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