PacBio smrtpipe commandline

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HOW TO run on the command line. 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.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

Common 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: 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): -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 cod5, 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 (if you can't find it, see below)
  • from the folder /projects/nscdata/smrtportal/userdata/jobs/016/, find the folder with your job number (it is most likely the job with the highest number)
  • copy the settings.xml file over to /projects/nscdata/scripts/pacbio/smrtpipe_xml_files/x.y.x/ (where x.y.z. is the version of smrtportal)
  • give it a smart name (check the other folders), e.g. filter_only_settings.xml, HGAP_settings.xml

Working with a reference for mapping

This part is based on information from Pacific Biosciences (accessed November 2013).

Some applications require a reference sequence, e.g. mapping for SNP calling and detecting base modifications, or for running Quiver for assembly polishing. smrtanalysis needs a reference repository for this, which you can create with the following command:

referenceUploader -c -p destination_folder -n short_name -f path/to/reference.fasta

For large genomes (probably anything larger than a bacterial genome), modify the command as such, to create a BLASR suffix array to speed up the mapping:

referenceUploader -c -p destination_folder -n short_name -f path/to/reference.fasta --saw='sawriter -welter'


  • several references can be added to the same destination_folder
  • pick a convenient short name
  • for large fasta files, building the index file takes some time (a 611 Mbp cod assembly fasta file took almost 2 hours)
  • when I do this, I get warnings about 'SLF4J', it seems these can be ignored

Using the reference repository

In the settings.xml file, there is a part saying:

<param name="reference" hidden="true">

Change the common/references/lambda part to the full path to the destination_folder