Bedtools map end with warning about a 'leading zero' error

Question

[Stephane Plaisance]

Dear,

I have a small issue with bedtools map trying to summarise counts per bins

My command

bedtools map -a filtered_Spurpurea_289_v1.0_100000-bin.bed -b filtered_Spurpurea_289_v1.0.bed -c 5 -o sum

My data is as follows

head filtered_Spurpurea_289_v1.0_100000-bin.bed

Scaffold0054    0    100000
Scaffold0054    100000    200000
Scaffold0054    200000    300000
Scaffold0054    300000    400000
Scaffold0054    400000    500000
Scaffold0054    500000    573197
Scaffold0055    0    100000
Scaffold0055    100000    200000
Scaffold0055    200000    300000
Scaffold0055    300000    400000

head filtered_Spurpurea_289_v1.0.bed

Scaffold0054    10687    10693    GAAGAGC    1    +
Scaffold0054    30250    30256    GCTCTTC    1    +
Scaffold0054    53473    53479    GCTCTTC    1    +
Scaffold0054    57071    57077    GCTCTTC    1    +
Scaffold0054    62088    62094    GAAGAGC    1    +
Scaffold0054    86589    86595    GAAGAGC    1    +
Scaffold0054    94789    94795    GCTCTTC    1    +
Scaffold0054    102250    102256    GAAGAGC    1    +
Scaffold0054    126879    126885    GAAGAGC    1    +
Scaffold0054    137132    137138    GCTCTTC    1    +

The chromosomes have names as follows

Scaffold0054    573197
Scaffold0055    567644
Scaffold0089    477557
Scaffold0105    449683
Scaffold0117    425116
.......
Scaffold2872    20021
Scaffold2873    20012
Scaffold2874    20012
chr01    19572393
chr02    24320169
chr03    16670881
chr04    18662064
chr05    22696942
chr06    25754837
chr07    17080783
chr08    15903549
chr09    12685735
chr10    19080865
chr11    17358976
chr12    13739472
chr13    21044956
chr14    12497313
chr15    22594380
chr16    30168740
chr17    18259289
chr18    15208986
chr19    15878805

And all bed files are name+position sorted

***** WARNING: File filtered_Spurpurea_289_v1.0.bed has a record where naming convention (leading zero) is inconsistent with other files:
chr01    7417    7423    GCTCTTC    1    +

This Is not due to the 0 in 'chr01', when I remove the '0' I get a different error on the same line

***** WARNING: File filtered_Spurpurea_289_v1.0.bed has inconsistent naming convention for record:
chr1    7417    7423    GCTCTTC    1    +

Thanks in advance

[Devon Ryan]

Does filtered_Spurpurea_289_v1.0_100000-bin.bed have chr01 and so on in it? Does using the -nonamecheck option help?