PacBioToCA no output

nanto · 09-12-2012, 07:47 AM

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?

sagarutturkar · 02-02-2013, 07:02 PM

Hi nanto,

any luck to resolve above problem? I am facing same problem.

nanto · 02-04-2013, 07:10 AM

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

sagarutturkar · 02-04-2013, 07:16 AM

Quote:

Originally Posted by nanto

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.

joh04207 · 04-15-2014, 01:19 PM

Quote:

Originally Posted by sagarutturkar

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.

pawel.osipowski · 04-15-2014, 02:35 PM

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

migrau · 06-15-2014, 07:35 PM

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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09-12-2012, 07:47 AM	#1
nanto Member Location: Wageningen, Netherlands Join Date: Sep 2012 Posts: 19	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?

02-02-2013, 07:02 PM	#2
sagarutturkar Member Location: Tennessee, USA Join Date: Sep 2010 Posts: 61	HI Hi nanto, any luck to resolve above problem? I am facing same problem.

02-04-2013, 07:10 AM	#3
nanto Member Location: Wageningen, Netherlands Join Date: Sep 2012 Posts: 19	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 07:19 AM.

04-15-2014, 02:35 PM	#6
pawel.osipowski Junior Member Location: Warsaw, Poland Join Date: Apr 2013 Posts: 2	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

06-15-2014, 07:35 PM	#7
migrau Junior Member Location: moon Join Date: Jun 2014 Posts: 4	In my case, it was because my data had not enougth overlaps, so the fasta ouput file was empty. Check log files.