Grokbase Groups Pig user April 2013
FAQ
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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  • KALLURI, RAJESH K (AG/1000) at Apr 22, 2013 at 9:19 pm
    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
    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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  • j.barrett Strausser at Apr 22, 2013 at 9:20 pm
    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 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
  • Mehmet Belgin at Apr 22, 2013 at 9:55 pm
    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
  • j.barrett Strausser at Apr 22, 2013 at 10:09 pm
    Glad it worked.

    -b

    On Mon, Apr 22, 2013 at 5:54 PM, Mehmet Belgin 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

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