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Old 07-02-2013, 06:23 AM   #1
Shishir
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Default Relating OrthoMCL clusters with Phylogenetics

I need to relate the OrthoMCL clusters (that I derived from comparison of several insect proteomes) with phylogenetic tree but I am not able to understand how to proceed? I would appreciate your suggestions.
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Old 07-02-2013, 07:28 AM   #2
rhinoceros
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Read this, get ideas
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Old 02-06-2015, 09:24 AM   #3
sarwar
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You find single copy genes in all the genome using orthomcl. Align all the genes within family and concatenate using MSA tools (muscel) and then concatenate and use distane calculating software like phylip and phyml and drawtree.
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Old 02-09-2015, 01:57 PM   #4
cascoamarillo
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Please, let me continue this post but talking about hal pipeline. So I saw it and decided to try it out. Though everything looks good (installation, dependencies), running the test_data I get an error:
Code:
You can inspect the inputs files that were used for this product, which are located in /bin/hal/test_data/errors/aligned_clusters_2015-02-09-T17-10Z_72f3b05deff53ccdb0c1b0508b26925c/inputs
The following was supplied as input:
$VAR1 = {
          'alignment_program' => 'muscle',
          'cluster_fastas' => {
                                '50002' => 'cluster_fastas/50002',
                                '15006' => 'cluster_fastas/15006',
                                '50000' => 'cluster_fastas/50000',
                                '20005' => 'cluster_fastas/20005',
                                '50003' => 'cluster_fastas/50003',
                                '40004' => 'cluster_fastas/40004',
                                '50001' => 'cluster_fastas/50001'
                              }
        };
The output directories of the jobs that were ran for this product have been put here: /bin/hal/test_data/errors/aligned_clusters_2015-02-09-T17-10Z_72f3b05deff53ccdb0c1b0508b26925c/jobs


The following error was reported while working on this stage in the pipeline:
*****************************
job failed producing errors:
child exited with value 2
job failed producing errors:
child exited with value 2
job failed producing errors:
child exited with value 2
job failed producing errors:
child exited with value 2
job failed producing errors:
child exited with value 2
job failed producing errors:
child exited with value 2
job failed producing errors:
child exited with value 2
*****************************


Below is a stacktrace:
*****************************

*****************************
Looks like it gets unaligned_clusters, but not able to go forward with the alignment....I don't see any trouble with muscle at all.
I'd appreciate any feedback. Thanks

Last edited by cascoamarillo; 02-09-2015 at 03:11 PM.
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Old 02-09-2015, 10:22 PM   #5
rhinoceros
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Quote:
Originally Posted by cascoamarillo View Post
Looks like it gets unaligned_clusters, but not able to go forward with the alignment....I don't see any trouble with muscle at all.
I'd appreciate any feedback. Thanks
It could be related to the stable bug. The stable option was removed from later versions of muscle but hal depends on a version that has it..
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Old 02-10-2015, 08:08 AM   #6
cascoamarillo
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Not sure. stable seems to be working well.
hal is using muscle 3.6; I've run it independently with the same parameters and inputs (-maxiters 16, -stable, -quiet) and so far they look good.

Edited: maybe it is. Run with clustalw instead; works.

Last edited by cascoamarillo; 02-10-2015 at 09:20 AM.
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