PacBio data set error

[MLister1]

Hi

I am trying to use the metamos software to analyse some pacbio data. When I try to run the pipeline I get this message:

Starting Task = preprocess.PREPROCESS *** metAMOS: Error: cannot correct without Celera Assembler and BLASR Oops, MetAMOS finished with errors! see text in red above for details.

Above that is the following warnings:

/cm/shared/apps/python/2.7.3/lib/python2.7/site-packages/setuptools-5.4.1-py2.7.egg/pkg_resources.py:1049: UserWarning: /panfs/panasas01.panfs.cluster/mrxml5/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).

Starting metAMOS pipeline Warning: BLASR is not found, some functionality will not be available Warning: Newbler is not found, some functionality will not be available Warning: MetaGeneMark is not found, some functionality will not be available Warning: SignalP+ is not found, some functionality will not be available Warning: metaphylerClassify is not found, some functionality will not be available Warning: PhyloSift was not found, will not be available

Warning: EA-UTILS is not found, some functionality will not be available Warning: R package is not found, some functionality will not be available

This is the code I used

initPipeline -q -1 VPI.css.fastq -d VPIPacbio -i 20:1300 -W imetAMOS

runPipeline -d VPIPacbio -t PBcR

I am assuming that the issue is that BLASTR is not available for some reason, what is likely to be the problem? Also is there any issues with the code as a starting point?

Many thanks, Michelle

[skoren]

Hi,

metAMOS will rely on Celera Assembler to generate corrected sequences and then assemble them. However, it has a slightly outdated version of Celera Assembler in the 1.5 release that relies on BLASR (the PacBio read aligner) to find overlaps between PacBio reads. More recent versions of Celera Assembler don’t need BLASR. You would have to install SMRTportal from PacBio or just BLASR to use PacBio within metAMOS. The main downside is that you would be used an older version of the Celera Assembler so you might be better off running the latest version manually and providing the contigs as input to metAMOS.

Serge

On Nov 20, 2015, at 6:55 AM, MLister1 [email protected] wrote:

Hi

I am trying to use the metamos software to analyse some pacbio data. When I try to run the pipeline I get this message:

Starting Task = preprocess.PREPROCESS *** metAMOS: Error: cannot correct without Celera Assembler and BLASR Oops, MetAMOS finished with errors! see text in red above for details.

Above that is the following warnings:

/cm/shared/apps/python/2.7.3/lib/python2.7/site-packages/setuptools-5.4.1-py2.7.egg/pkg_resources.py:1049: UserWarning: /panfs/panasas01.panfs.cluster/mrxml5/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).

Starting metAMOS pipeline Warning: BLASR is not found, some functionality will not be available Warning: Newbler is not found, some functionality will not be available Warning: MetaGeneMark is not found, some functionality will not be available Warning: SignalP+ is not found, some functionality will not be available Warning: metaphylerClassify is not found, some functionality will not be available Warning: PhyloSift was not found, will not be available

Warning: EA-UTILS is not found, some functionality will not be available Warning: R package is not found, some functionality will not be available

This is the code I used

initPipeline -q -1 VPI.css.fastq -d VPIPacbio -i 20:1300 -W imetAMOS

runPipeline -d VPIPacbio -t PBcR

I am assuming that the issue is that BLASTR is not available for some reason, what is likely to be the problem? Also is there any issues with the code as a starting point?

Many thanks, Michelle

— Reply to this email directly or view it on GitHub https://github.com/marbl/metAMOS/issues/232.