[jvilj]

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

my $bwapath = "$Bin"."/bwa/bwa";

to

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!

[MPatel]

Hello boetsie,

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

Thank you.

[MPatel]

Thank you boetsie.

I will give a try changing bowtie/bwa execution permissions. let see if it works.

[boetsie]

I think it has something to do with the user rights of bowtie/bwa.

[MPatel]

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

[namigrt]

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

[gwilkie]

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!

[gwilkie]

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

[stepa_t]

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

[gwilkie]

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?

[gwilkie]

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

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

[weijenc]

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

[gwilkie]

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

[weijenc]

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

[stepa_t]

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