Fail to write VCF file - negative coordinates

[eudesbarbosa]

Issue
For a couple of my samples I had problems while writing the MEIs to VCF, negative coordinate issue. Library kit: 'Agilent SureSelect Human All Exon V8'. Could you please help me deal with this issue?

scramble.sh --ref /path/to/hs37d5.fa --out-name /path/to/targeted_seq_mei_calling/work/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1/out/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1 --cluster-file /path/to/targeted_seq_mei_calling/work/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1/out/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1_cluster.txt --nCluster 5 --mei-score 50 --indel-score 80 --poly-a-frac 0.75 --eval-meis
Running sample: /path/to/targeted_seq_mei_calling/work/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1/out/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1_cluster.txt
Running scramble with options:
INSTALL.DIR : /path/to/targeted_seq_mei_calling/.snakemake/conda/9154f892d04f9bfe82a4d010855d834d/share/scramble/bin
blastRef : /path/to/hs37d5.fa
clusterFile : /path/to/targeted_seq_mei_calling/work/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1/out/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1_cluster.txt
deletions : FALSE
indelScore : 80
mei.refs : /path/to/targeted_seq_mei_calling/.snakemake/conda/9154f892d04f9bfe82a4d010855d834d/share/scramble/resources/MEI_consensus_seqs.fa
meiScore : 50
meis : TRUE
minDelLen : 50
nCluster : 5
no.vcf : FALSE
outFilePrefix : /path/to/targeted_seq_mei_calling/work/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1/out/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1
pctAlign : 90
polyAFrac : 0.75
polyAdist : 100
Useful Functions Loaded
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Done analyzing l1
Done analyzing sva
Done analyzing alu
Done analyzing l1
Done analyzing sva
Done analyzing alu
Sample had 38 MEI(s)
Done analyzing MEIs
Writing VCF file to /path/to/targeted_seq_mei_calling/work/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1/out/bwa.scramble.<SAMPLE_ID>-N1-DNA1-WES1.vcf...
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord,  :
  solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (0) is < 1
Calls: write.scramble.vcf ... make_IRanges_from_windows_args -> solveUserSEW -> .Call2

[minn333]

I got the same error messages for many files:

Writing VCF file to $PATH/${SampleName}.scramble.vcf...
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord, :
solving row 1: 'allow.nonnarrowing' is FALSE and the supplied start (0) is < 1
Calls: write.scramble.vcf ... make_IRanges_from_windows_args -> solveUserSEW -> .Call2
Execution halted

[zyha]

Hey,
I believe this happens when MEI is detected at 0th position of the chromosome. We can interpret the nucleotide before the first in the chromosome as 'N'. It resolved after I added the following code in the make.vcf.R

if (start == 0) return('N')
add to this function
get_refs = function(fa, chrom, start, end){ if (start == 0) return('N') ... }

[minn333]

thank you. Jessica ***@***.***> 於 2023年3月17日 週五 下午12:36 寫道：

…

Hey, I believe this happens when MEI is detected at 0th position of the chromosome. We can interpret the nucleotide before the first in the chromosome as 'N'. It resolved after I added the following code in the make.vcf.R get_refs = function(fa, chrom, start, end){ if (start == 0) return('N') ... } — Reply to this email directly, view it on GitHub <#29 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOUUAAPXBCWEZP3HXSNRKVLW4PS3DANCNFSM6AAAAAAQQ2PCM4> . You are receiving this because you commented.Message ID: ***@***.***>