Error: map::at

[raagagrawal]

Running SeqKat with the following command results in the error:

Error:
Error: map::at

Command:
seqkat(
sigcutoff = 5,
mutdistance = 3.2,
segnum = 4,
ref.dir = '/hot/user/ragrawal/reference/GRCh38-BI-20160721/',
bed.file = example.bed.file,
output.dir = "/hot/user/ragrawal/Liss-Agrawal-PRAD-COLB/kataegis/seqkat_output",
chromosome = "4",
chromosome.length.file = '/hot/user/ragrawal/Liss-Agrawal-PRAD-COLB/kataegis/seqkat_input/chromosome_lengths.txt',
trinucleotide.count.file = '/hot/user/ragrawal/Liss-Agrawal-PRAD-COLB/kataegis/seqkat_input/trinucleotide_counts.txt')

BED file is from the package itself:
example.bed.file <- paste0(
path.package("SeqKat"),
"/extdata/test/PD4120a-chr4-1-2000000_test_snvs.bed"
);

Chromosome length file looks like this:
num length
1 248956422
2 242193529
3 198295559
4 190214555
5 181538259
6 170805979
7 159345973
8 145138636
9 138394717
10 133797422
11 135086622
12 133275309
13 114364328
14 107043718
15 101991189
16 90338345
17 83257441
18 80373285
19 58617616
20 64444167
21 46709983
22 50818468
23 156040895
24 57227415
sum.f 3031042417
sum.m 3088269832

Trinucleotide Count file looks like this:
trinucleotide count
AAA 111989738
AAC 43201194
AAG 58189769
AAT 72371689
ACA 58990692
ACC 33696401
ACG 7493615
ACT 47217592
AGA 65098960
AGC 40871572
AGG 51544445
AGT 47153556
ATA 60052604
ATC 38913595
ATG 53392579
ATT 72972218
CAA 55028101
CAC 43811665
CAG 59422990
CAT 53647632
CCA 53187843
CCC 37938793
CCG 7997076
CCT 51686199
CGA 6476677
CGC 6973826
CGG 8163775
CGT 7538164
CTA 37526148
CTC 49233040
CTG 58845855
CTT 58949909
GAA 58550174
GAC 27584997
GAG 49296690
GAT 39318178
GCA 42251785
GCC 34400705
GCG 7021186
GCT 40553684
GGA 45711130
GGC 34385793
GGG 38041000
GGT 33680960
GTA 33111127
GTC 27376011
GTG 44271034
GTT 42931358
TAA 60184362
TAC 32800448
TAG 37758992
TAT 59993479
TCA 57480061
TCC 44773999
TCG 6640570
TCT 65097477
TGA 57463257
TGC 41996189
TGG 54069670
TGT 59316856
TTA 60047401
TTC 58469576
TTG 56336500
TTT 113221598

[tyamaguchi-ucla]

@raagagrawal I think the example was probably built with GRCh37 while GRCh38 was used as reference.

[raagagrawal]

@tyamaguchi-ucla Yep! Could be the explanation for the example.bed. This also fails w/ the same error code with my sample .bed file. Path: /hot/user/ragrawal/Liss-Agrawal-PRAD-COLB/kataegis/seqkat_input/BCLB_snvs.bed.