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Old 12-01-2014, 08:02 AM   #1
rusty1947
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Default Size issue of Pacbio Reads

Hello everyone,

I have pacbio reads for a bacteria in fastq format of size 2.6 G. I wanted to run a denovo assembly using SPAdes. I used the basic command for running an unpaired pacbio read which is

$./spades.py -s Pacbio.fastq -o /home/spades_run

The issue I am facing now is that it is taking too long for the reads to assemble. Can anyone suggest how to reduce the run time?

Thank you
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Old 12-01-2014, 09:51 AM   #2
luc
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Did you run your reads through HGAP first?
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Old 12-01-2014, 09:59 AM   #3
rusty1947
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Hello Luc,
Its my understanding that HGAP requires .h5 files which i do not have. I just have the fastq files
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Old 12-01-2014, 10:07 AM   #4
luc
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In this case I would try to run SPRAI first:
http://zombie.cb.k.u-tokyo.ac.jp/sprai/README.html
and try to get the h5 files anyhow.
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Old 12-02-2014, 09:43 AM   #5
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Another option is PBcR (Celera Assembler) use MHAP for the overlapping and the assembly should complete in a couple of hours on a single 16 core machine.
+1 for getting the h5, you will need the information in the h5 to run quiver and get a high quality consensus for the final assembly.
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Old 12-04-2014, 06:21 AM   #6
rusty1947
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Thank you luc and rhall. I will try these programs.
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Old 12-05-2014, 07:30 AM   #7
rusty1947
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Hello,

I am not sure if I should start a new thread for this. but since it is an issue surrounding PBcR I thought I would continue here. I tried using PBcR command on my pacbio.fastq. This is what I used

$wgs-8.2/Linux-amd64/bin/PBcR -length 500 -partitions 200 -l S_pacbio -s /wgs-8.2/Linux-amd64/bin/sampleData/pacbio.spec -fastq pacbio.fastq genomeSize=2800000

It abruptly ends and I am getting the S_pacbio.fastq file as

Cannot open self /home/kvaviko/bin/wgs-8.2/Linux-amd64/bin/falcon_sense or archive /home/kvaviko/bin/wgs-8.2/Linux-amd64/bin/falcon_sense.pkg
+
]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]

Has anyone encountered this problem before?
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Old 12-10-2014, 03:01 PM   #8
tnn11
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Default Falcon_Sense

I have the same problem;

"Cannot open self" from falcon_sense. And it's there......
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Old 12-10-2014, 03:34 PM   #9
rhall
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For PBcR bugs http://sourceforge.net/p/wgs-assembler/bugs/ is probably a better place to post things like this.
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Old 12-10-2014, 03:50 PM   #10
GenoMax
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Check permissions on those files (since they are in bin they will likely need execute permissions, add for all). We recently ran into issues where file permissions were not correctly set for some components of SMRTportal by default install process.
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Old 12-12-2014, 10:35 AM   #11
rusty1947
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Hello,

So i was able to fix the Falcon_sense issue. Apparently the pipeline had some issues with the falcon_sense pkg in december. One of the developers of PBcR suggested to download the precompiled binaries for CA 8.2 again from the website. I ran PBcR again after downloading the latest PBcR and I am no longer running into that problem.

Hope this helps.
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Old 01-11-2015, 12:59 PM   #12
akorobeynikov
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Quote:
Originally Posted by rusty1947 View Post
Hello everyone,

I have pacbio reads for a bacteria in fastq format of size 2.6 G. I wanted to run a denovo assembly using SPAdes. I used the basic command for running an unpaired pacbio read which is

$./spades.py -s Pacbio.fastq -o /home/spades_run

The issue I am facing now is that it is taking too long for the reads to assemble. Can anyone suggest how to reduce the run time?

Thank you
SPAdes cannot be used for de novo assembly of PacBio reads alone (unless you have pre-corrected or CCS reads). As stated in the manual, SPAdes performs *hybrid* assembly of your Illumina / IonTorrent + PacBio data.
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