Problem using Bowtie : Warning: Empty input file Reference file does not seem to be a FASTA file

Question

[Bioinfo]

Hello Everyone , i hope you're doing well

i'm using Gap Filler , after scaffolding , in LIbrary file i specefied Bowtie for mapping , but it didn't work i ve got this error message :

ITERATION 1:

=>Sat Apr 18 18:10:40 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

i don't know what went wrong , my reference File seems to be in Fasta file

[ATpoint]

Please post the full command line and a head of your problematic file. This is standard for debugging questions, please do it as default in the future.

[Bioinfo]

Thank you for your reply heres the command 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

scaffold2|size98566

scaffold3|size96881 and so on

[ATpoint]

That is not a fasta file. A fasta is like

>name1
sequence...
>name2 
sequence...

I am not into assembly myself but the tool apparently wants a fasta file from your previous assembly the contains the sequences of the scaffolds. Is this available to you?

[Bioinfo]

yes it's like you said

scaffold1|size99433
 sequence
scaffold2|size98566
 sequence
scaffold3|size96881 and so on
 sequnece

...