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De novo alignement with smrttools

Hello,

I work with smrttools and the tools hgap4 to make a de novo alignement.

This my command line :

pbcromwell run pb_hgap4 -e /home/my.subreadset.xml --task-option HGAP_GenomeLength_str 13000000 --nproc 32 --config /home/cromwell.conf

The problem is with the option HGAP_GenomeLength_str . I got :

pbcromwell: error: unrecognized arguments: 13000000

I don't know what syntax to use to add this argument. I had many tries : HGAP_GenomeLength_str = 13000000 ; HGAP_GenomeLength_str '13000000' ; HGAP_GenomeLength_str = [13000000] ..... But it still doesn't work.

Any help?

denovo alignment smrttools
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written by pablo pablo

My best guess based on the manual is HGAP_GenomeLength_str=13000000 without any whitespaces.

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written by ATpoint ATpoint

Hi @pablo, can you give a bit more information, where in cromewell.conf file you add this information?

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written by SP SP

2 answers

Actually, to run this kind of smrttools pipeline, you need to insert a cromwell.conf file in the command line. It includes settings, paramaters ... I found a solution : I don't put the HGAP_GenomeLength_str=13000000 in the command line but in that file. Cause even if I put the option HGAP_GenomeLength_str=13000000 in the commande line, it does not work.

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written by pablo pablo

Hi @SP , I first defined the cromwell.conf file with pbcromwell configure --default-backend Local --output-file cromwell.conf , then I used that command line pbcromwell run pb_hgap4 -e subreadset.xml --config full/path/cromwell.conf --output-dir output_assembly

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written by pablo pablo

Thank you for replying, one more question, where (under which tag) do you add HGAP_GenomeLength_str=13000000 parameter in the cromwell.conf file. Thank you in advance

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written by SP SP

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