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Posted to user@pig.apache.org by Mehmet Belgin <me...@oit.gatech.edu> on 2013/04/22 23:06:37 UTC
Pig cannot resolve BamUDFLoader
Hi Everyone,
I have absolutely no experience with Pig and limited experience with hadoop, so please bear with me. We built a small hadoop cluster for experimental purposes and installed pig with all listed dependencies. I made sure that all of the jars are in CLASSPATH and env variables are defined as docuemtned, but still getting the following error:
2013-04-22 16:50:08,770 [main] ERROR org.apache.pig.tools.grunt.Grunt - ERROR 1070: Could not resolve BamUDFLoader using imports: [, org.apache.pig.builtin., org.apache.pig.impl.builtin.]
And this is the command we are running:
pig -param inputfile=./bowtie_sorted.bam -param outputfile=hadoop_bam.pileup -param pparallel=1 ${SEQPIG_HOME}/scripts/pileup.pig
My google search for this error or "BamUDFLoader" alone did not return anything useful. Which jar is supposed to provide this function? Any suggestions will be appreciated.
Thanks a lot in advance!
-Mehmet
RE: Pig cannot resolve BamUDFLoader
Posted by "KALLURI, RAJESH K (AG/1000)" <ra...@monsanto.com>.
What is the .bam file your are trying to load as and how is it generated?
What does your pig script look like? That will help answer your question.
-----Original Message-----
From: Mehmet Belgin [mailto:mehmet.belgin@oit.gatech.edu]
Sent: Monday, April 22, 2013 4:07 PM
To: user@pig.apache.org
Subject: Pig cannot resolve BamUDFLoader
Hi Everyone,
I have absolutely no experience with Pig and limited experience with hadoop, so please bear with me. We built a small hadoop cluster for experimental purposes and installed pig with all listed dependencies. I made sure that all of the jars are in CLASSPATH and env variables are defined as docuemtned, but still getting the following error:
2013-04-22 16:50:08,770 [main] ERROR org.apache.pig.tools.grunt.Grunt - ERROR 1070: Could not resolve BamUDFLoader using imports: [, org.apache.pig.builtin., org.apache.pig.impl.builtin.]
And this is the command we are running:
pig -param inputfile=./bowtie_sorted.bam -param outputfile=hadoop_bam.pileup -param pparallel=1 ${SEQPIG_HOME}/scripts/pileup.pig
My google search for this error or "BamUDFLoader" alone did not return anything useful. Which jar is supposed to provide this function? Any suggestions will be appreciated.
Thanks a lot in advance!
-Mehmet
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Re: Pig cannot resolve BamUDFLoader
Posted by "j.barrett Strausser" <j....@gmail.com>.
Glad it worked.
-b
On Mon, Apr 22, 2013 at 5:54 PM, Mehmet Belgin <mehmet.belgin@oit.gatech.edu
> wrote:
> Oh, I assumed that seqpig was a part of pig.
>
> Replacing the "pig" with "seqpig" did the trick. Looks like the args are
> identical to those of the pig.
>
> Thank you for your responses!
>
> -Mehmet
>
>
>
> On Apr 22, 2013, at 5:20 PM, j.barrett Strausser wrote:
>
> > Looks like that loader is related to and available from :
> > http://seqpig.sourceforge.net/
> >
> > I don't believe the BamUdfLoader is native to pig.
> >
> > -b
> >
> >
> > On Mon, Apr 22, 2013 at 5:06 PM, Mehmet Belgin <
> mehmet.belgin@oit.gatech.edu
> >> wrote:
> >
> >> Hi Everyone,
> >>
> >> I have absolutely no experience with Pig and limited experience with
> >> hadoop, so please bear with me. We built a small hadoop cluster for
> >> experimental purposes and installed pig with all listed dependencies. I
> >> made sure that all of the jars are in CLASSPATH and env variables are
> >> defined as docuemtned, but still getting the following error:
> >>
> >> 2013-04-22 16:50:08,770 [main] ERROR org.apache.pig.tools.grunt.Grunt -
> >> ERROR 1070: Could not resolve BamUDFLoader using imports: [,
> >> org.apache.pig.builtin., org.apache.pig.impl.builtin.]
> >>
> >> And this is the command we are running:
> >>
> >> pig -param inputfile=./bowtie_sorted.bam -param
> >> outputfile=hadoop_bam.pileup -param pparallel=1
> >> ${SEQPIG_HOME}/scripts/pileup.pig
> >>
> >> My google search for this error or "BamUDFLoader" alone did not return
> >> anything useful. Which jar is supposed to provide this function? Any
> >> suggestions will be appreciated.
> >>
> >> Thanks a lot in advance!
> >> -Mehmet
> >>
> >>
> >>
> >>
> >
> >
> > --
> >
> >
> > https://github.com/bearrito
> > @barrettsmash
>
>
--
https://github.com/bearrito
@barrettsmash
Re: Pig cannot resolve BamUDFLoader
Posted by Mehmet Belgin <me...@oit.gatech.edu>.
Oh, I assumed that seqpig was a part of pig.
Replacing the "pig" with "seqpig" did the trick. Looks like the args are identical to those of the pig.
Thank you for your responses!
-Mehmet
On Apr 22, 2013, at 5:20 PM, j.barrett Strausser wrote:
> Looks like that loader is related to and available from :
> http://seqpig.sourceforge.net/
>
> I don't believe the BamUdfLoader is native to pig.
>
> -b
>
>
> On Mon, Apr 22, 2013 at 5:06 PM, Mehmet Belgin <mehmet.belgin@oit.gatech.edu
>> wrote:
>
>> Hi Everyone,
>>
>> I have absolutely no experience with Pig and limited experience with
>> hadoop, so please bear with me. We built a small hadoop cluster for
>> experimental purposes and installed pig with all listed dependencies. I
>> made sure that all of the jars are in CLASSPATH and env variables are
>> defined as docuemtned, but still getting the following error:
>>
>> 2013-04-22 16:50:08,770 [main] ERROR org.apache.pig.tools.grunt.Grunt -
>> ERROR 1070: Could not resolve BamUDFLoader using imports: [,
>> org.apache.pig.builtin., org.apache.pig.impl.builtin.]
>>
>> And this is the command we are running:
>>
>> pig -param inputfile=./bowtie_sorted.bam -param
>> outputfile=hadoop_bam.pileup -param pparallel=1
>> ${SEQPIG_HOME}/scripts/pileup.pig
>>
>> My google search for this error or "BamUDFLoader" alone did not return
>> anything useful. Which jar is supposed to provide this function? Any
>> suggestions will be appreciated.
>>
>> Thanks a lot in advance!
>> -Mehmet
>>
>>
>>
>>
>
>
> --
>
>
> https://github.com/bearrito
> @barrettsmash
Re: Pig cannot resolve BamUDFLoader
Posted by "j.barrett Strausser" <j....@gmail.com>.
Looks like that loader is related to and available from :
http://seqpig.sourceforge.net/
I don't believe the BamUdfLoader is native to pig.
-b
On Mon, Apr 22, 2013 at 5:06 PM, Mehmet Belgin <mehmet.belgin@oit.gatech.edu
> wrote:
> Hi Everyone,
>
> I have absolutely no experience with Pig and limited experience with
> hadoop, so please bear with me. We built a small hadoop cluster for
> experimental purposes and installed pig with all listed dependencies. I
> made sure that all of the jars are in CLASSPATH and env variables are
> defined as docuemtned, but still getting the following error:
>
> 2013-04-22 16:50:08,770 [main] ERROR org.apache.pig.tools.grunt.Grunt -
> ERROR 1070: Could not resolve BamUDFLoader using imports: [,
> org.apache.pig.builtin., org.apache.pig.impl.builtin.]
>
> And this is the command we are running:
>
> pig -param inputfile=./bowtie_sorted.bam -param
> outputfile=hadoop_bam.pileup -param pparallel=1
> ${SEQPIG_HOME}/scripts/pileup.pig
>
> My google search for this error or "BamUDFLoader" alone did not return
> anything useful. Which jar is supposed to provide this function? Any
> suggestions will be appreciated.
>
> Thanks a lot in advance!
> -Mehmet
>
>
>
>
--
https://github.com/bearrito
@barrettsmash