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Old 04-05-2013, 03:08 AM   #21
CPCantalapiedra
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Quote:
Originally Posted by megancamilla View Post
Hey CPCantalarpiedra,

I'm having exactly the same problem. Can you elaborate on how you fixed your problem? Did you remove a symbolic link or put one in? Also in which directory is your bwa and bowtie installed? (i.e. /usr/local/bin?)

Thanks!

Megan
Umm maybe not the best way to do this, but I am working with the full path and the program in my local bin, so... ~/bin/GapFiller_v1-11_linux-x86_64/GapFiller.pl
bwa and bowtie are already in the same GapFiller folder. I hope this helps
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Old 04-05-2013, 03:35 AM   #22
heath.obrien
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Quote:
Originally Posted by boetsie View Post
Hmmm, that is very strange. Any idea if the scaffolds contain very short sequences between gaps, e.g.;

AAGCTGCTAGNNNGTATGNNNNNAGGGTAGATAG

I think the script does not handle these patterns very well at the moment. I'm working on this.

Regards,
Boetsie
Most of the truncated sequences do not have short sequences between gaps, but they do have short sequences between the start of the scaffold and the first N. There also appears to be a relationship between the length of this sequence and the size of the truncated sequence.
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Old 04-22-2013, 10:11 AM   #23
rebecca_m_d
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Hi Boetsie,

I have been using SSPACE for scaffolding, and I would like to try your new software for gap filling. But first, I need help in understanding the final evidence from SSPACE. Can you please explain the example below? 1st line... Reverse of contig_93 has 17 links to forward of contig_17. But, is there an estimated gap of 164bp or an overlap of 164bp between contigs? The sequence region in question does not have lower case bases (indicating an overlap), but has only 1 lower case "n". Should I interpret all the lowercase n's as potential gaps? Have you been able to validate these gaps in the lab?

>scaffold16.1|size67863|tigs4
r_tig93|size18643|links17|gaps-164
f_tig17|size46195|links7|gaps-164
f_tig266|size1908|links15|gaps-169
r_tig282|size1114

Thanks in advance for your help!
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Old 06-13-2013, 03:04 AM   #24
stepa_t
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Default BWA error on MacOS

Hi all,

I've tried to run GapFiller on MacOS 10.6.8 and got the bwa error (similar to described above by CPCantalapiedra:

message on shell is:

=>Thu Jun 13 13:54:34 2013: Mapping reads to scaffolds, reading alignment output and storing reads

and there is tmpbwa_logfile which states:
Bwa error; -1 at /BFX/GapFiller_v1-11_linux-x86_64/GapFiller.pl line 218.

Could you please help?

Many thanks in advance!
Cheers,
Stepan
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Old 06-20-2013, 03:59 AM   #25
weijenc
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Default Is it required to error-correct the reads?

Hello,

I am about to use GapFiller (very exciting). Is it advised to error-correct the paired-end reads, or even filter them, before running GapFiller?

Many thanks,


WJ
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Old 06-25-2013, 08:32 AM   #26
gwilkie
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Hi, I'm setting up to try out GapFiller. I've previously been using IMAGE for extension and filling of assembly gaps with reasonable success.

Please can you tell me if there is a manual for GapFiller? In particular I don't understand how to make the library file (two paired-read files with insert size, error and orientation indication) and I can't find any help for this.

Thanks,
Gavin
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Old 06-25-2013, 09:19 AM   #27
weijenc
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gwilkie,

How did you make IMAGE work?! I tried it and it was very unstable on my system.... It stopped randomly.

To your question, in the tar ball coming with GapFiller there's a README file explaining everything. You can find instruction on how to construct your library file. It's pretty straight forward.

WH
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Old 06-25-2013, 09:39 AM   #28
gwilkie
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Thanks WH, thats much appreciated

I didn't get the GapFiller readme from our sysadmin, so I'll have a look for the the file now.

I'm afraid that our (excellent) sysadmin guy installed IMAGE (I don't have root access myself). However I do recall he had a very difficult time getting it to work on BioLinux. It assumes that your system is set up in a particular fashion, but ours has a different architecture. He ended up modifying the source code quite a lot to make it point in the correct places for the other software IMAGE relies on. It took him quite a few tries before he was successful. This was more than a year ago, and before the release of PAGIT pipeline from Sanger that IMAGE is now a part of. Perhaps if you install the entire PAGIT package you might have better luck?

Sorry I can't be of more help, I'm one of those pesky Biologists who dabble in Bioinformatics and only have fairly basic UNIX skills!

Best wishes,
Gavin

Quote:
Originally Posted by weijenc View Post
gwilkie,

How did you make IMAGE work?! I tried it and it was very unstable on my system.... It stopped randomly.

To your question, in the tar ball coming with GapFiller there's a README file explaining everything. You can find instruction on how to construct your library file. It's pretty straight forward.

WH
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Old 07-11-2013, 07:58 AM   #29
gwilkie
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I have been trying to get GapFiller to run, but I get the same error as Stepa_t.

It stops at iteration 1 after printing
=>Thu Jul 11 16:49:06 2013: Mapping reads to scaffolds, reading alignment output and storing reads

In the tmpbwa_logfile
Bwa error; -1 at /software/bin/GapFiller line 218.

Can anyone assist - is it failing to find bwa? bwa is installed on our BioLinux system but perhaps GapFiller is looking in the wrong place?

Last edited by gwilkie; 07-11-2013 at 08:04 AM. Reason: mistake
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Old 07-12-2013, 12:54 AM   #30
stepa_t
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Quote:
Originally Posted by gwilkie View Post
I have been trying to get GapFiller to run, but I get the same error as Stepa_t.

It stops at iteration 1 after printing
=>Thu Jul 11 16:49:06 2013: Mapping reads to scaffolds, reading alignment output and storing reads

In the tmpbwa_logfile
Bwa error; -1 at /software/bin/GapFiller line 218.

Can anyone assist - is it failing to find bwa? bwa is installed on our BioLinux system but perhaps GapFiller is looking in the wrong place?
Hi Gavin,

Finally I got this running by changing bwa folder by new bwa version http://bio-bwa.sourceforge.net/

Hope this helps.
Cheers,
Stepan
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Old 07-12-2013, 08:42 AM   #31
gwilkie
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GapFiller is now working thanks to our wonderful Bioinformatics people

The software was looking in the wrong folder for bwa, so they changed to script for me and now it points to the correct place on our server.

Initial testing shows that GapFiller is much, much faster than IMAGE and it is also easier to run and interpret the results. Top stuff, and thanks to the developers. I'll be using this a lot to improve my assemblies!

Cheers, Gavin
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Old 07-15-2013, 05:01 AM   #32
gwilkie
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Not only is GapFiller faster and easier to run than IMAGE, my initial testing also shows that it closes more gaps in my assemblies. Excellent!
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Old 09-10-2013, 07:09 PM   #33
namigrt
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Quote:
Originally Posted by mcnelson.phd View Post
I've been trying to get GapFiller working on a number of Illumina assemblies that we have in my lab, but I'm not getting all of the output files that the manual says I should.

I ran the tutorial on the scaffolds in the example/ folder using the stipulated read sets, but I never get the following output files: XXX.filler.final.text, XXX.closed.evidence.txt, XXX.gapfilled.final.fa.

I do get the following files: XXX.summarfile.final.txt, XXX.gapclosure.fa and a bwa logfile in alignoutput/ and an empty XXX.closed.evidence.iteration1.txt file in intermediate_results/.

Has anyone else had this problem or have any suggestions for getting the correct output files?
Hi

Im trying to use GapFiller program and am facing the same problem. Was this issue solved. If yes, could you please let me know what the issue was.

Thanks
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Old 11-08-2013, 04:12 AM   #34
MPatel
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Exclamation GapFiller Stops after 1st ITERATION

Hello,

I am new to this thread. I have been using SSPACE for scaffolding and its been fantastic. Now I am trying GapFiller to close the gaps in scaffolds. But some how it stops after 1st Iteration on Mac OS 10.7 however it runs smoothly on linux with the same parameters.

I dont know why its not working on Mac.

Any ideas....

Thank you...

MPatel
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Old 11-08-2013, 07:37 AM   #35
boetsie
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I think it has something to do with the user rights of bowtie/bwa.
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Old 11-08-2013, 08:29 AM   #36
MPatel
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Thank you boetsie.

I will give a try changing bowtie/bwa execution permissions. let see if it works.
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Old 11-11-2013, 03:22 AM   #37
MPatel
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Hello boetsie,

Its working smoothly now. I have downloaded bwa and bowtie and it worked.

Thank you.
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Old 02-11-2014, 02:48 AM   #38
jvilj
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Quote:
Originally Posted by gwilkie View Post
I have been trying to get GapFiller to run, but I get the same error as Stepa_t.

It stops at iteration 1 after printing
=>Thu Jul 11 16:49:06 2013: Mapping reads to scaffolds, reading alignment output and storing reads

In the tmpbwa_logfile
Bwa error; -1 at /software/bin/GapFiller line 218.

Can anyone assist - is it failing to find bwa? bwa is installed on our BioLinux system but perhaps GapFiller is looking in the wrong place?

It appears that GapFiller expects `bwa` to be in the folder that it was called from. I've changed `GapFiller.pl` at line 212 from
Code:
my $bwapath = "$Bin"."/bwa/bwa";
to
Code:
my $bwapath = "bwa";
(since `bwa` is on my path), and it is running smoothly now. I guess one could also specify the full path to `bwa`, e.g. "~/src/bwa-0.7.5a/bwa".

@CPCantalapiedra @gwilkie: Thanks for pointing me in the right direction!

@boetsie: Thanks for the nice software!
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Old 02-20-2014, 07:18 PM   #39
shuixia100
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Quote:
Originally Posted by lizzyzhao View Post
Hi Marten,

Thanks for the tool for gap filling. However, I had some problem running it , basically the problem is it stopped at the the bowtie-build which is the first step of bowtie. I checked the align output file, it turned out that asem1.contig.gpfill.gapclosure.fa is empty. I tried to read through your perl script but failed to understand how asem1.contig.gpfill.gapclosure.fa is generated so I couldn't figure out why this is empty. Could you please let me know the possible reason of it? Thank you very much!

-rw-r--r-- 1 users 40 2013-03-08 06:10 asem1.contig.gpfill.bowtieIndex.1.ebwt
-rw-r--r-- 1 users 4 2013-03-08 06:10 asem1.contig.gpfill.bowtieIndex.2.ebwt
-rw-r--r-- 1 users 0 2013-03-08 06:10 asem1.contig.gpfill.gapclosure.fa



perl ~/bin/GapFiller_v1-11_linux-x86_64/GapFiller.pl -l libraries -s asem1.contig -m 30 -o 3 -r 0.7 -n 10 -d 50 -t 0 -g 0 -T 1 -i 1 -b asem1.contig.gpfill

Your inserted inputs on [GapFiller_v1-11_Final] at Fri Mar 8 05:37:25 2013:
-s asem1.contig
-l libraries
-b asem1.contig.gpfill
-o 3
-m 30
-r 0.7
-n 10
-T 1
-g 0
-d 50
-t 0
-i 1


=>Fri Mar 8 05:37:25 2013: Reading and processing paired-read files

ITERATION 1:

=>Fri Mar 8 06:10:25 2013: Mapping reads to scaffolds, reading alignment output and storing reads
Warning: Empty input file
Reference file does not seem to be a FASTA file
Command: /home/bin/GapFiller_v1-11_linux-x86_64/bowtie/bowtie-build --quiet --noref asem1.contig.gpfill/alignoutput/asem1.contig.gpfill.gapclosure.fa asem1.contig.gpfill/alignoutput/asem1.contig.gpfill.bowtieIndex

Bowtie-build error; 256 at /home/bin/GapFiller_v1-11_linux-x86_64/GapFiller.pl line 242.
I am having same problem. did you figure out how to fix it?
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Old 03-14-2014, 02:16 AM   #40
Dagga
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Thanks for the tips! I have finally got this program working.

I was wondering if anyone has any tips on a starting region for the error settings that are inputted into the library file.

I have a bacterial genome approximately 9Mb in size using an insert size of ~400-500.

I know it will be variable but I was just after a good place to start. I noticed the manual uses 0.25 but this is with an insert size of 1000.

Anyway, any opinions on where to start would be helpful thanks!
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