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uclahs-cds / public-R-SeqKat

Detection of Kataegis
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Error: map::at #3

Open raagagrawal opened 1 year ago

raagagrawal commented 1 year ago

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 commented 1 year ago

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

raagagrawal commented 1 year ago

@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.