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Old 08-08-2016, 07:49 PM   #3
lingling huang
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Location: changsha

Join Date: Mar 2016
Posts: 46
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Quote:
Originally Posted by Magdoll View Post
Hi,

Short answer is yes. There are multiple ways to hack tofu_wrap.py -- will require additional monitoring of the parallel jobs. But I first need to ask what parameters did you use to call tofu_wrap.py? What are the size bins (aka what are the subdirectories in clusterOut/)? Do you have an SGE cluster? Do you have multiple nodes from which you can run parallel pbtranscript.py cluster jobs?

Also, please consider joining the Iso-Seq google group: https://groups.google.com/forum/#!forum/smrt_isoseq

Since tofu_wrap.py is on the cutting edge (it's not officially supported in SMRTAnalysis 2.x but is on the agenda for SMRTAnalysis 3.x), the google group is better suited

--Liz
Code:
tofu_wrap.py --nfl_fa isoseq_nfl.fasta --ccs_fofn reads_of_insert.fofn --bas_fofn input.fofn -d clusterOut --quiver --bin_manual "(0,2,4,6,8,9,10,11,12,13,15,17,19,20,23)" --gmap_db /zs32/data-analysis/liucy_group/llhuang/Reflib/gmapdb --gmap_name gmapdb_h19 --output_seqid_prefix human isoseq_flnc.fasta final.consensus.fa
The lab's sever is high-powered single-node computer and
has no an SGE cluster. Can I use multiple CPUs to run command?
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