organizing a Bed file for bedtools getfasta

Question

[oldtownroald]

I am trying to use bedtools getfasta on some bed files, but the issue is that the peaks bed file columns are mixed up such that the first column with the chromosome names contains the peak location as well for some of the chromosomes. How can I reorganize the bed file so that the chromosome names are separated from the peak locations and etc.

This is an output I received while running the bedtools getfasta command.

Feature (3R:7071004-7071004) has length = 0, Skipping.
Feature (3R:7072290-7072290) has length = 0, Skipping.
Feature (3R:3298414-3298414) has length = 0, Skipping.

Thanks!

[ATpoint]

Please show conent of the file.

[oldtownroald]

This is what the top few lines look like:

trackname = "rnaedit_WXLib05_01_AG2.txt.threshold.threshold" description = "test description" visibility=2 color=0,0,0 useScore=0
3R  1685256 1685256 10%_28r 107.142857143   3R   1685256     CG41099     EXON    0   25  3   0   28  0   26  0   0   26  3   28  0   26  10.7142857143   107.142857143   10%_28r     3R_1685256
3R  1686077 1686077 29%_24r 291.666666667   3R   1686077     CG41099     EXON    0   16  7   1   24  0   14  0   0   14  7   24  0   14  29.1666666667   291.666666667   29%_24r     3R_1686077
2L  10993267    10993267    15%_20r 150.0   2L   10993267    CG16833     EXON    17  0   0   3   20  40  0   0   0   40  3   20  0   40  15.0    150.0   15%_20r     2L_10993267
2L  10993814    10993814    14%_27r 148.148148148   2L   10993814    CG16833     EXON    23  0   0   4   27  25  0   0   0   25  4   27  0   25  14.8148148148   148.148148148   14%_27r     2L_10993814

[ATpoint]

That is not a BED file. Is must not contain a header. Try removing that and please show the command line.