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4.0 years ago
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Hello i m using Gap Filler after scaffolding using sspace i specified Bowtie in the library but is shows erro msg :
ITERATION 1:
=>Sat Apr 18 20:55:12 2020: Mapping reads to scaffolds, reading bowtie output and storing unmapped reads
Warning: Empty input file
Reference file does not seem to be a FASTA file
Command: /GapFiller_v1-10_linux-x86_64/bowtie/bowtie-build --quiet --noref GapFiller_RESULTS/alignoutput GapFiller_RESULTS.1.gapclosure.fa GapFiller_RESULTS/alignoutput/ GapFiller_RESULTS.Lib1.1.bowtieIndex
Bowtie-build error; 256 242
Here's the commands i used
GapFiller.pl -l Gap_Filler_Library -s file.fasta -m 30 -b GapFiller_RESULTS -t 4
and here's the lubrary file
Lib1 bowtie R_1_Miseq.fastq R_2_Miseq.fastq 400 0.25 FR
and here's the header of the scaffold file
>scaffold1|size99433
sequence
>scaffold2|size98566
sequence
>scaffold3|size96881
sequence
and so on Please Help , Thank you
I think there's extra spaces between your directory and file names!
Does your scaffold file contain scaffolds too? Because the one you posted seems to only contain headers.
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer
If that is the exact header then are
>missing from fasta header names?Hello , thanks for reply NO there s ">" in the headers , what i didn't find is the NNNNNN maybe that why it show s this error message , when i created a new file containing the same content of thi previous one with some NNNNN... , and i run gapfiller, it didn't show the error message. still i don't know why sspace output doesn't have NNNN in the sequence