bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
Error in .width_as_unnamed_integer(width, msg = "an end that is greater or equal to its start minus one") :
each range must have an end that is greater or equal to its start minus one
Calls: GRanges ... .new_IRanges_from_start_end -> .width_as_unnamed_integer
Execution halted
awk '$3 < $2' *_CNVs
1 21609560 1243169 2 gain AB 21.2881
1 16063512 3785230 10 gain AAAAAAAAAB 97.5609
1 6186631 187245 2 gain - -1
1 25370404 1485153 4 gain AABB 16.2339
2 68945341 21013533 2 gain AB 7.00891
2 29003494 11144128 2 gain AA 100
4 48149537 124697 2 gain - -1
6 30105129 8415011 2 gain AB 12.8361
6 8416866 486768 3 gain - -1
7 65398809 817552 3 gain - -1
14 49832172 20476585 2 gain AA 9.9227
15 33870907 19973204 2 gain - -1
16 7518112 88882 5 gain - -1
17 8743610 5338153 2 gain AB 5.33086
18 13059066 2847946 2 gain - -1
21 13349244 5585983 2 gain - -1
X 15531318 2266942 0 loss - -1
X 2291481 318831 1 gain A -1
X 2789590 1632846 1 gain A -1
X 40738165 15566377 1 gain A -1
X 36348130 13735370 1 gain A -1
X 13736510 2949752 1 gain A -1
Y 9530385 1381151 0 loss - -1
ControlFreec produces incorrect entries, unsure why.
nextflow run nf-core/sarek \
-r 3.9.0 \
-profile mamba \
--genome GATK.GRCh38 \
--input samplesheet.csv \
--outdir results \
--igenomes_base /groups/genomics/ref_genome/igenomes/references \
--wes \
--intervals /groups/genomics/genomics_analysis/sarek_pipeline/WES_Targets/SureSelect_v8_hg38.bed \
-c /home/sarek_pipeline/nf_config/nextflow.config \
-c /groups/genomics/genomics_analysis/sarek_pipeline/controlfreec/controlfreec.config \
--vep_cache /groups/genomics/vep \
--snpeff_cache /groups/genomics/snpeff/snpEff/data/GRCh38.99 \
--step variant_calling \
--tools controlfreec \
--cf_coeff 0.1 \
--cf_contamination_adjustment true \
--cf_ploidy 1,2,3,4,5
Description of the bug
ControlFreec produces incorrect entries, unsure why.
Command used and terminal output
Relevant files
No response
System information
No response