Gapfiller Error : Failed To Fill The Gap

Question

[HG]

Hi everybody, I am doing some plasmid assembly with Spades. After getting the scaffold form Spades i was trying to fill the gap insilico with GapFiller but i am getting error like that : My library file looks like :

lib200 bwa R27_S1_L001_R1_001.fastq R27_S1_L001_R2_001.fastq 214 0.25 FR`enter code here`

Error

[bwa_index] Pack FASTA... [bns_fasta2bntseq] zero length sequence. Abort!
Aborted (core dumped)

Bwa error; 34304 at GapFiller.pl line 218.

But once i am trying with same parameter with GapFiller example data its running fine with same parameter.

Please help me out

Answer 1

[Istvan Albert]

You are making use of an empty file or an incorrect path to the sequence - note how the error comes from not being able to index the fasta file that you pass there.

Try to run the bwa index directly on that file and see what happens:

Answer 2

[wpwupingwp]

Same problem

It seems that GapFiller could only recognize SSPACE's output, while other fasta files it can't read or just tell you that this is an empty file.

However, I tried to edit id of every sequence in my fasta file, to make it looks same with SSPACE's result fasta, but it doesn't work, either.

cat tmpbwa_logfile
[bwa_index] Pack FASTA... [bns_fasta2bntseq] zero length sequence. Abort!

Bwa error; 134 at GapFiller.pl line 220

Answer 3

[5heikki]

I had the same problem with GapFiller, i.e. the example data worked but my own did not. Then finally I realized that the input fasta file absolutely must include gaps to fill, i.e. seqs with "NNNNNNNNN" in the middle. If you don't have that, the zero length error message can not be avoided. The program literally does what the name implies, it fills gaps.