Return-Path: X-Original-To: apmail-hadoop-mapreduce-user-archive@minotaur.apache.org Delivered-To: apmail-hadoop-mapreduce-user-archive@minotaur.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id E4FCA1050A for ; Mon, 9 Sep 2013 16:35:52 +0000 (UTC) Received: (qmail 38350 invoked by uid 500); 9 Sep 2013 16:35:46 -0000 Delivered-To: apmail-hadoop-mapreduce-user-archive@hadoop.apache.org Received: (qmail 38270 invoked by uid 500); 9 Sep 2013 16:35:43 -0000 Mailing-List: contact user-help@hadoop.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@hadoop.apache.org Delivered-To: mailing list user@hadoop.apache.org Received: (qmail 38251 invoked by uid 99); 9 Sep 2013 16:35:40 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 09 Sep 2013 16:35:40 +0000 X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: domain of felipe.o.gutierrez@gmail.com designates 209.85.216.53 as permitted sender) Received: from [209.85.216.53] (HELO mail-qa0-f53.google.com) (209.85.216.53) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 09 Sep 2013 16:35:35 +0000 Received: by mail-qa0-f53.google.com with SMTP id ii20so314021qab.12 for ; Mon, 09 Sep 2013 09:35:14 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=iVz3259q1aWF1lFQ7b9O6Z/hvebRZ52/TwqsXLLVx9w=; b=VFMWGaRddUxQF2mkm39eoA0LuXWV9slBkbDdZH2dKXeQP7e2fyphHsS0uwDBKtpShF 36EYuLIOxsnCGRz7OXBfTBzu5hqgV5qCmndwFACBIinZAaKfjRVHTqE6mUMaR5Quj0DM m1xBEqWwzPUn3eLM8jhQgfae5y3inXZmqlYMYx9qZ8ela45mWTIipXE4VAyfblOXIK54 r/IoTiOxLgWKRCSE6VAH9/KyEiyBmC5rEbGXrRiRGAeQZeZybfksD3XwF7Fmak8aWYqt qlYZMCGdB0OFlaCZr3Wx2m9891KxqS8osWOs7s0OASaMaC3BPBTSvenh69Wci4E0Bg5e sXAA== MIME-Version: 1.0 X-Received: by 10.224.167.211 with SMTP id r19mr2629621qay.18.1378744514497; Mon, 09 Sep 2013 09:35:14 -0700 (PDT) Received: by 10.49.5.165 with HTTP; Mon, 9 Sep 2013 09:35:14 -0700 (PDT) In-Reply-To: References: Date: Mon, 9 Sep 2013 13:35:14 -0300 Message-ID: Subject: Re: Running Contrail on hadoop From: Felipe Gutierrez To: user@hadoop.apache.org Content-Type: multipart/alternative; boundary=089e0149c6a605d42504e5f5f9ce X-Virus-Checked: Checked by ClamAV on apache.org --089e0149c6a605d42504e5f5f9ce Content-Type: text/plain; charset=ISO-8859-1 Since I didn't get to work with Contrail, I started to learn CloudBurst. http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst After one hour learning I could run MpReduce jobs on Hadoop. :) Felipe On Mon, Sep 9, 2013 at 11:59 AM, Felipe Gutierrez < felipe.o.gutierrez@gmail.com> wrote: > Hi, I set the locale and after this I tryied to execute again the > Contrail, but the results are files with size zero. > > Have antbody already runned Contrail on Hadoop? > Thanks > Felipe > > $ bin/hadoop jar contrail-1.0-SNAPSHOT.jar contrail.Contrail -asm assembly > -k 25 -reads /user/hduser/reads/small.fq > Contrail 0.8.2 > > ================================================================================== > Input: /user/hduser/reads/small.fq > Workdir: assembly/ > ... > ... > ... > $ bin/hadoop jar contrail-1.0-SNAPSHOT.jar contrail.BuildGraph -k 25 > -input /user/hduser/reads/small.fq -output /user/hduser/output -asm > /user/hduser/assembly -reads /user/hduser/reads/small.fq > 13/09/09 11:50:11 INFO contrail.BuildGraph: Tool name: BuildGraph > 13/09/09 11:50:11 INFO contrail.BuildGraph: - input: > /user/hduser/reads/small.fq > 13/09/09 11:50:11 INFO contrail.BuildGraph: - output: /user/hduser/output > 13/09/09 11:50:12 WARN mapred.JobClient: Use GenericOptionsParser for > parsing the arguments. Applications should implement Tool for the same. > 13/09/09 11:50:12 INFO util.NativeCodeLoader: Loaded the native-hadoop > library > 13/09/09 11:50:12 WARN snappy.LoadSnappy: Snappy native library not loaded > 13/09/09 11:50:12 INFO mapred.FileInputFormat: Total input paths to > process : 1 > 13/09/09 11:50:12 INFO mapred.JobClient: Running job: job_201309030936_0068 > 13/09/09 11:50:13 INFO mapred.JobClient: map 0% reduce 0% > 13/09/09 11:50:18 INFO mapred.JobClient: map 3% reduce 0% > ... > ... > ... > hduser@cloud6:/usr/local/hadoop$ bin/hadoop fs -ls /user/hduser/output > Found 52 items > -rw-r--r-- 3 hduser supergroup 0 2013-09-09 11:55 > /user/hduser/output/_SUCCESS > drwxr-xr-x - hduser supergroup 0 2013-09-09 11:50 > /user/hduser/output/_logs > -rw-r--r-- 3 hduser supergroup 0 2013-09-09 11:51 > /user/hduser/output/part-00000 > ... > ... > > > > On Sat, Sep 7, 2013 at 2:44 PM, Jens Scheidtmann < > jens.scheidtmann@gmail.com> wrote: > >> Dear Felipe, >> >> Did you set the locale on all machines of the cluster? >> >> Best regards, >> >> Jens >> > > > > -- > *-- > -- Felipe Oliveira Gutierrez > -- Felipe.o.Gutierrez@gmail.com > -- https://sites.google.com/site/lipe82/Home/diaadia* > -- *-- -- Felipe Oliveira Gutierrez -- Felipe.o.Gutierrez@gmail.com -- https://sites.google.com/site/lipe82/Home/diaadia* --089e0149c6a605d42504e5f5f9ce Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Since I didn't get to work with Contrail, I started to= learn CloudBurst.=A0http://sourceforge.net/apps/mediawi= ki/cloudburst-bio/index.php?title=3DCloudBurst
After one hour learning I could run MpReduce jobs on Hadoop. :)

Felipe

=
On Mon, Sep 9, 2013 at 11:59 AM, Felipe Guti= errez <felipe.o.gutierrez@gmail.com> wrote:
Hi, I set the locale and af= ter this I tryied to execute again the Contrail, but the results are files = with=A0size=A0zero.

Have antbody already runned Contrail on Hadoop?
Th= anks
Felipe

$ bin/hadoop jar contrail-1.0-SNAPS= HOT.jar contrail.Contrail -asm assembly -k 25 -reads /user/hduser/reads/sma= ll.fq
Contrail 0.8.2
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Input: /user/hduser/reads/small.fq
Workdir: assembly/
<= /div>
...
...
...
$ bin/hadoop jar c= ontrail-1.0-SNAPSHOT.jar contrail.BuildGraph -k 25 -input /user/hduser/read= s/small.fq -output /user/hduser/output -asm /user/hduser/assembly -reads /u= ser/hduser/reads/small.fq
13/09/09 11:50:11 INFO contrail.BuildGraph: Tool name: BuildGraph
13/09/09 11:50:11 INFO contrail.BuildGraph: =A0- input: /user/hduser/= reads/small.fq
13/09/09 11:50:11 INFO contrail.BuildGraph: =A0- o= utput: /user/hduser/output
13/09/09 11:50:12 WARN mapred.JobClient: Use GenericOptionsParser for = parsing the arguments. Applications should implement Tool for the same.
13/09/09 11:50:12 INFO util.NativeCodeLoader: Loaded the native-hado= op library
13/09/09 11:50:12 WARN snappy.LoadSnappy: Snappy native library not lo= aded
13/09/09 11:50:12 INFO mapred.FileInputFormat: Total input p= aths to process : 1
13/09/09 11:50:12 INFO mapred.JobClient: Runn= ing job: job_201309030936_0068
13/09/09 11:50:13 INFO mapred.JobClient: =A0map 0% reduce 0%
13/09/09 11:50:18 INFO mapred.JobClient: =A0map 3% reduce 0%
...
...
...
hduser@cloud6:/usr/local/= hadoop$ bin/hadoop fs -ls /user/hduser/output
Found 52 items
-rw-r--r-- =A0 3 hduser supergroup =A0 =A0 = =A0 =A0 =A00 2013-09-09 11:55 /user/hduser/output/_SUCCESS
drwxr-= xr-x =A0 - hduser supergroup =A0 =A0 =A0 =A0 =A00 2013-09-09 11:50 /user/hd= user/output/_logs
-rw-r--r-- =A0 3 hduser supergroup =A0 =A0 =A0 =A0 =A00 2013-09-09 11:= 51 /user/hduser/output/part-00000
...
...

=

On Sat, Sep 7, 2013 at 2:44 PM, Jens Scheidtmann <jens.scheidtman= n@gmail.com> wrote:
Dear Felipe,

Did you set the l= ocale on all machines of the cluster?

Best regards= ,

Jens






--
--
-- = Felipe Oliveira Gutierrez
-- Felipe.o.Gutierrez@gmail.com
-- https://= sites.google.com/site/lipe82/Home/diaadia
--089e0149c6a605d42504e5f5f9ce--