Difference between revisions of "PacBio smrtpipe commandline"

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(Created page with "=== HOW TO run smrtpipe.py on the command line. === smrtpipe.py is the PacBio pipeline for filtering and mapping PacBio runs, as well as running HGAP. For filtering-only jobs, ...")
 
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Actual filtering (NPROC is the number of CPUs the job gets):  
 
Actual filtering (NPROC is the number of CPUs the job gets):  
<pre>smrtpipe.py -D TMP=./ -D SHARED_DIR=./ -D NPROC=24 --params=settings.xml xml:input.xml &amp;&gt; smrtpipe.err</pre>  
+
<pre>smrtpipe.py -D TMP=./ -D SHARED_DIR=./ -D NPROC=24 --params=desired_settings.xml xml:input.xml &amp;&gt; smrtpipe.err</pre>  
 
=== How to obtain the settings.xml file  ===
 
=== How to obtain the settings.xml file  ===
  

Revision as of 09:30, 25 October 2013

HOW TO run smrtpipe.py on the command line.

smrtpipe.py is the PacBio pipeline for filtering and mapping PacBio runs, as well as running HGAP. For filtering-only jobs, it splits the raw reads on the adaptor and generates all subreads in fasta or fastq format.

Input:

  • input.fofn, list of files to process (see below)
  • bax.h5 files (or, before 2.0 software version, bas.h5 files) from the run (one per movie), raw-output from the PacBio
  • a settings.xml file, see below, specifies the job. See the end of this page for how to obtain such a xml file


STEPS

set up environment

module load  smrtanalysis/x.y.z # at the time of writing, 'x.y.z' is 2.0.1

generate smrtcells.fofn file

find path/to/runfile|grep bax.h5 >smrtcells.fofn #NOTE for pre 2,0 versions, use 'bas.h5'!

convert this file to correct xml format:

fofnToSmrtpipeInput.py smrtcells.fofn >input.xml

copy a settings xml file, e.g. filter_only_settings.xml, HGAP_settings.xml, ...

rsync /projects/nscdata/scripts/pacbio/smrtpipe_xml_files/x.y.z/desired_settings.xml . 

NOTE won't work within a screen ..?

Actual filtering (NPROC is the number of CPUs the job gets):

smrtpipe.py -D TMP=./ -D SHARED_DIR=./ -D NPROC=24 --params=desired_settings.xml xml:input.xml &> smrtpipe.err

How to obtain the settings.xml file

After a smrtportal upgrade, if it is not yet there in the folder /projects/nscdata/scripts/pacbio/smrtpipe_xml_files

  • In SMRTportal on cod2, set up a job using the protocol you want to run, e.g. RS_Filter_Only, RS_HGAP_Assembly, you don't have to execute it
  • note down the job number
  • from the folder /projects/nscdata/smrtportal/userdata/jobs/016/, find the folder with your job number
  • copy the settings.xml file over to /projects/nscdata/scripts/pacbio/smrtpipe_xml_files/x.y.x/
  • give it a smart name (check the other folders), e.g. filter_only_settings.xml, HGAP_settings.xml