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Old 09-12-2012, 06:47 AM   #1
nanto
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Default PacBioToCA no output

I managed somehow to get frg files and so on.
But after this instruction:
./pacBioToCA -length 500 -partitions 200 -l pacbio -t 16 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg > run.out

The file is empty. How can I solve this?
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Old 02-02-2013, 06:02 PM   #2
sagarutturkar
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Default HI

Hi nanto,

any luck to resolve above problem? I am facing same problem.
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Old 02-04-2013, 06:10 AM   #3
nanto
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Yes, I remember, that somehow I did work out this problem on my own.

I will try getting the instructions from my notes. Since that time a lot happends, but I'm pretty sure I didn't throw out sth, on which I was working so hard.

Tomorrow or so, I would try posting what I will find.

EDIT:

Try getting sth useful from this:

fastqToCA -libraryname illumina - insertsize 200 60
-mates path,path > illumina12.frg
cat illumina12.frg
gatekeeper -T -o illumina12.gkpStore illumina12.frg
gatekeeper -dumpfragments -withsequence illumina12.gkpStore pbtest.fastq
cat test.gkpStore.fastqUIDmap
fastqToCA -libraryname pbtest -reads path > pbtest.frg
cat pbtest.frg
gatekeeper -T -o pbtest.gkpStore pbtest.frg
gatekeeper -dumpfragments -withsequence pbtest.gkpStore

pacbioToCA -length 500 -partitions 200 -l pbtest -t 1 -s path(to spec file) -fastq path(to fastq file) pbtest.illumina12.frg 2>&1 | tee --append pacbiotoca.log

Last edited by nanto; 02-04-2013 at 06:19 AM.
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Old 02-04-2013, 06:16 AM   #4
sagarutturkar
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Quote:
Originally Posted by nanto View Post
Yes, I remember, that somehow I did work out this problem on my own.

I will try getting the instructions from my notes. Since that time a lot happends, but I'm pretty sure I didn't throw out sth, on which I was working so hard.

Tomorrow or so, I would try posting what I will find.
Thanks nanto. I was able to run the correction with 454 data. The problem is with illumina data. It would be great if you share some tricks you did to correct with illumina data. Awaiting for your instructions.
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Old 04-15-2014, 12:19 PM   #5
joh04207
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Quote:
Originally Posted by sagarutturkar View Post
Thanks nanto. I was able to run the correction with 454 data. The problem is with illumina data. It would be great if you share some tricks you did to correct with illumina data. Awaiting for your instructions.
Did anyone ever have a resolution this this post? I am getting the same results with an Illumina file input. It has to be the format of this file since I can get PacBioToCA to work with a ccs file as the input. Can it be the quality formatting of the illumina fastq file? This came off of a recent MiSeq 2X300 run.
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Old 04-15-2014, 01:35 PM   #6
pawel.osipowski
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I think I've got similar problem with Illumina paired-end. I have no errors when launching pacBioToCA but it creates only run.out in given path with some useless info. .frg seems to be done correctly.

Pawel
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Old 06-15-2014, 06:35 PM   #7
migrau
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In my case, it was because my data had not enougth overlaps, so the fasta ouput file was empty. Check log files.
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