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Forum: Bioinformatics 09-17-2013, 03:23 PM
Replies: 0
Views: 1,084
Posted By 9000revs
Myrna 1.2.1 and Bowtie2 compatibility

Does Myrna work with latest Bowtie?

Thanks.
Forum: Bioinformatics 09-10-2013, 08:16 AM
Replies: 4
Views: 2,460
Posted By 9000revs
My problem got solved when I used the required...

My problem got solved when I used the required version of Bowtie 0.12.8. Please try that first.
Forum: Bioinformatics 08-23-2013, 12:36 PM
Replies: 3
Views: 2,163
Posted By 9000revs
Well, update to my thread, not much help here it...

Well, update to my thread, not much help here it seems.......

My problem was solved by running the job on a 3 node cluster as opposed to the 1 node cluster I was initially testing on (all nodes...
Forum: Bioinformatics 08-22-2013, 02:38 PM
Replies: 3
Views: 2,163
Posted By 9000revs
This is what I see when I run the install test: ...

This is what I see when I run the install test:

[root@idh-dev03 myrna-1.2.1]# ./myrna_hadoop --test
Searching for 'bowtie' binary...
Specified via --bowtie?....no
$MYRNA_BOWTIE_HOME...
Forum: Bioinformatics 08-22-2013, 10:20 AM
Replies: 3
Views: 2,163
Posted By 9000revs
More details from stderr, if it helps. ...

More details from stderr, if it helps.

Align.pl: s3cmd: found: , given:
Align.pl: jar: found: /usr/java/latest/bin/jar, given:
Align.pl: hadoop: found: /usr/lib/hadoop/libexec/../bin/hadoop,...
Forum: Bioinformatics 08-20-2013, 11:43 AM
Replies: 3
Views: 2,163
Posted By 9000revs
Myrna 1.2.1 on Hadoop problems

Please help ......

Have installed Myrna 1.2.1 on Hadoop cluster (0.20) with Bowtie 1.0.0, R/BioConductor and SRA toolkits. All required env variables have been set. Install tests pass fine. When...
Forum: Bioinformatics 08-20-2013, 09:31 AM
Replies: 4
Views: 1,847
Posted By 9000revs
Once you installed SRA toolkit, did you set the...

Once you installed SRA toolkit, did you set the env variable called MYRNA_SRATOOLKIT_HOME?
Forum: Bioinformatics 08-20-2013, 09:19 AM
Replies: 6
Views: 2,690
Posted By 9000revs
Did you install the SRA toolkit and set the env...

Did you install the SRA toolkit and set the env var MYRNA_SRATOOLKIT_HOME?
Forum: Bioinformatics 08-20-2013, 09:14 AM
Replies: 2
Views: 1,844
Posted By 9000revs
I had similar issues with Crossbow on CDH4. It...

I had similar issues with Crossbow on CDH4. It worked on CDH3 (which is the 0.02x ver of Hadoop as mentioned as pre-req for this).
Forum: Bioinformatics 08-19-2013, 10:45 AM
Replies: 2
Views: 2,376
Posted By 9000revs
Thanks to Micheal S, I was able to obtain the...

Thanks to Micheal S, I was able to obtain the specific bowtie 0.12.8 and everything seems to work fine. Hadoop errors are really bogus! :)
Forum: Bioinformatics 07-24-2013, 10:37 AM
Replies: 3
Views: 1,587
Posted By 9000revs
Hi Narain: Can you please provide more...

Hi Narain:

Can you please provide more details on what version of cluster you made CB work on? If you see my posts, I have been having all kinds of issues with hadoop and CB.

Thanks.
Forum: Bioinformatics 07-24-2013, 08:47 AM
Replies: 2
Views: 2,376
Posted By 9000revs
Crossbow 1.2.1 On Hadoop - question

I am running this on a CDH3 cluster currently.

Crossbow prerequisites mention the following among others:

1. A bowtie v0.12.8 executable must exist at the same path on all cluster nodes...
Forum: Bioinformatics 07-09-2013, 12:29 PM
Replies: 4
Views: 2,460
Posted By 9000revs
Is this a Hadoop configuration error? Standard...

Is this a Hadoop configuration error? Standard hadoop tests like Terasort, Wordcount work fine. Any help is greatly appreciated. Thanks.
Forum: Bioinformatics 06-28-2013, 08:47 AM
Replies: 4
Views: 2,460
Posted By 9000revs
New error observed this morning trying to re-run...

New error observed this morning trying to re-run the example - "Broken Pipe"!!! :)

org.apache.hadoop.streaming.PipeMapRed: java.io.IOException: Broken pipe
at...
Forum: Bioinformatics 06-27-2013, 12:15 PM
Replies: 4
Views: 2,460
Posted By 9000revs
Crossbow 1.2.1 On Hadoop - help needed

We have installed a Crossbow 1.2.1 on our 3 node Hadoop Cluster [running Intel Hadoop Distrib]. After installation, I ran the sample test script ./cb_hadoop –test and that validated that all...
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