[mcnelson.phd]

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?

[CPCantalapiedra]

I had the same problem sometimes. Don't know exactly why, but running again the analysis often works in my case, and the complete output file set is generated. You can try to run with several iterations and you can check in the output which iteration is stopping at. Maybe stderr could give some light too?

[boetsie]

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, somehow gapFiller stopped at a certain point. Can you look at the command line at see if there is any error?

Regards,Boetsie

[boetsie]

Hi Martin,

I have been working with GapFiller and had great success with the first assembly that I tried it on, but I'm having a puzzling problem with my latest run: a large number of the contigs are being dramatically truncated. Before running GapFiller, the minimum contig size was 200 bp, but after running it there are over 1200 contigs shorter than 100 bp, with some as short as 2 bp. Do you (or anyone else) have any idea what might be going on here? I ran it with the default parameters.

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

[megancamilla]

GapFiller doesn't go through iterations

umm when pasting the bowtie line I realized that maybe the symbolik link was causing the problem, and it seems that it was the source of the problem in both cases.

Also, could you explain further when and what for using iterations? I have checked and the second iteration is closing gaps, so it seems useful. Why weren't closed during iteration1? It is just the discovery of previously unmapped reads, that now are able to completely map to one edge?

Thank you again!
CPC

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

[CPCantalapiedra]

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

[heath.obrien]

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.

[rebecca_m_d]

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!

[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

[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

[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]

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]

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

[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?

[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