Hi,
I was trying to run IReNA on my data and got the following error while running the last steps. Can you please suggest what can be the reason
############################## Code #####################################
library(IReNA)
BiocManager::install("org.Hs.eg.db")
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
calculate cuts of each each position in footprints
bamfilepath1 <- 'CM_filter.bam'
test_clustering <- readRDS("Kmeans_clustering_ENS.rds")
#txbd=TxDb.Mmusculus.UCSC.mm10.knownGene
#motif=Tranfac201803_Mm_MotifTFsF
#Combine all footprints of motifs
combined <- combine_footprints("fimo_out/")
head(combined)
peak <- read.table("p2g_filtered_peaks.txt")
overlapped <- overlap_footprints_peaks(combined, peak)
#filtered_footprints <- read.table("filtered_footprints1.bed")
#head(overlapped)
#saveRDS(overlapped,"overlapped_footprints.rds")
#asked for overlapped footprints that overlaps with peaks
list1 <- get_related_genes(footprints=overlapped,txdb=TxDb.Hsapiens.UCSC.hg38.knownGene,motif=Tranfac201803_Hs_MotifTFsF,Species = 'Hs')
list2<-get_related_peaks(list1,test_clustering)
list2
set parameter 'workers' to make this function run in parallel
cuts1 <- cal_footprint_cuts(bamfilepath = bamfilepath1,index_bam = FALSE, bedfile = list2[[1]],workers = 16)
##########################################################################
################################ Error #####################################
'select()' returned 1:many mapping between keys and columns
Error in checkForRemoteErrors(val) :
6 nodes produced errors; first error: replacement has length zero
Calls: cal_footprint_cuts ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Execution halted
############################## output #####################################
sequence_name start stop strand p.value matched_sequence motif_id
1 chr1 1906463 1906477 + 2.57e-05 AGTGCAGATGGGCTG M00002
2 chr1 3772662 3772676 - 8.95e-05 CCGGAAGGTGGCGGG M00002
3 chr1 3772678 3772692 - 9.15e-05 CGGGGAGGTGTCTGG M00002
4 chr1 6236008 6236022 - 9.63e-05 CGGGCAGCTGCCCTT M00002
5 chr1 6236009 6236023 + 6.29e-05 AGGGCAGCTGCCCGC M00002
6 chr1 11273438 11273452 - 9.65e-05 GGGGCAGCAGGGCCC M00002
preparing features information... 2025-02-18 11:02:52
identifying nearest features... 2025-02-18 11:02:53
calculating distance from peak to TSS... 2025-02-18 11:03:06
assigning genomic annotation... 2025-02-18 11:03:06
adding gene annotation... 2025-02-18 11:03:34
'select()' returned 1:many mapping between keys and columns
assigning chromosome lengths 2025-02-18 11:03:35
done... 2025-02-18 11:03:35
[[1]]
sequence_name V5 V6
228 chr1 100132882 100133002
229 chr1 100132864 100133024
230 chr1 100132855 100133035
231 chr1 100132837 100133057
232 chr1 100132856 100133036
233 chr1 100132843 100133053
234 chr1 100132838 100133058
235 chr1 100132884 100133004
236 chr1 100132839 100133059
237 chr1 100132858 100133038
.
.
.
50567 chr1 179954688 179954838
50568 chr1 179954688 179954838
50569 chr1 179954670 179954860
50570 chr1 179954656 179954876
50571 chr1 179954702 179954822
50572 chr1 179954680 179954850
[ reached 'max' / getOption("max.print") -- omitted 881809 rows ]
[[2]]
V3 V4 V5 PeakGene V7 V8
228 chr1 100132937 100132948 ENSG00000156876|Promoter 100132882 100133002
229 chr1 100132937 100132952 ENSG00000156876|Promoter 100132864 100133024
230 chr1 100132937 100132954 ENSG00000156876|Promoter 100132855 100133035
231 chr1 100132937 100132958 ENSG00000156876|Promoter 100132837 100133057
232 chr1 100132938 100132955 ENSG00000156876|Promoter 100132856 100133036
233 chr1 100132938 100132958 ENSG00000156876|Promoter 100132843 100133053
234 chr1 100132938 100132959 ENSG00000156876|Promoter 100132838 100133058
235 chr1 100132939 100132950 ENSG00000156876|Promoter 100132884 100133004
236 chr1 100132939 100132960 ENSG00000156876|Promoter 100132839 100133059
237 chr1 100132940 100132957 ENSG00000156876|Promoter 100132858 100133038
238 chr1 100132940 100132959 ENSG00000156876|Promoter 100132849 100133049
239 chr1 100132940 100132961 ENSG00000156876|Promoter 100132840 100133060
240 chr1 100132941 100132954 ENSG00000156876|Promoter 100132877 100133017
241 chr1 100132941 100132956 ENSG00000156876|Promoter 100132868 100133028
242 chr1 100132944 100132965 ENSG00000156876|Promoter 100132844 100133064
243 chr1 100132946 100132967 ENSG00000156876|Promoter 100132846 100133066
244 chr1 100132948 100132958 ENSG00000156876|Promoter 100132898 100133008
245 chr1 100132948 100132959 ENSG00000156876|Promoter 100132893 100133013
246 chr1 100132948 100132960 ENSG00000156876|Promoter 100132889 100133019
247 chr1 100132948 100132960 ENSG00000156876|Promoter 100132889 100133019
.
.
.
23653 chr1 151909442 151909463 ENSG00000159445|Promoter 151909342 151909562
23654 chr1 151909444 151909450 ENSG00000159445|Promoter 151909412 151909482
23655 chr1 151909449 151909459 ENSG00000159445|Promoter 151909399 151909509
23656 chr1 151909449 151909460 ENSG00000159445|Promoter 151909394 151909514
23657 chr1 151909450 151909456 ENSG00000159445|Promoter 151909418 151909488
23658 chr1 151909450 151909470 ENSG00000159445|Promoter 151909355 151909565
23659 chr1 151909452 151909463 ENSG00000159445|Promoter 151909397 151909517
23660 chr1 151909453 151909468 ENSG00000159445|Promoter 151909380 151909540
23661 chr1 151909454 151909475 ENSG00000159445|Promoter 151909354 151909574
23662 chr1 151909455 151909466 ENSG00000159445|Promoter 151909400 151909520
23663 chr1 151909455 151909469 ENSG00000159445|Promoter 151909387 151909537
23664 chr1 151909456 151909469 ENSG00000159445|Promoter 151909392 151909532
23665 chr1 151909456 151909479 ENSG00000159445|Promoter 151909347 151909587
23666 chr1 151909457 151909469 ENSG00000159445|Promoter 151909398 151909528
23667 chr1 151909457 151909470 ENSG00000159445|Promoter 151909393 151909533
V9
228 M05891;ENSG00000197343
229 M09727;ENSG00000064703
230 M06193;ENSG00000152926
231 M09984;ENSG00000103495
232 M06193;ENSG00000152926
233 M07141;ENSG00000006194
234 M09984;ENSG00000103495
235 M06172;ENSG00000184939;ENSG00000 213988|M06223;ENSG00000204920|M06609;ENSG00000187626
236
.
.
.
M10375;ENSG00000185591
23666 M10176;ENSG00000087510
23667 M09591;ENSG00000087510
[ reached 'max' / getOption("max.print") -- omitted 900857 rows ]
Hi,
I was trying to run IReNA on my data and got the following error while running the last steps. Can you please suggest what can be the reason
############################## Code #####################################
library(IReNA)
BiocManager::install("org.Hs.eg.db")
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)
calculate cuts of each each position in footprints
bamfilepath1 <- 'CM_filter.bam'
test_clustering <- readRDS("Kmeans_clustering_ENS.rds")
#txbd=TxDb.Mmusculus.UCSC.mm10.knownGene
#motif=Tranfac201803_Mm_MotifTFsF
#Combine all footprints of motifs
combined <- combine_footprints("fimo_out/")
head(combined)
peak <- read.table("p2g_filtered_peaks.txt")
overlapped <- overlap_footprints_peaks(combined, peak)
#filtered_footprints <- read.table("filtered_footprints1.bed")
#head(overlapped)
#saveRDS(overlapped,"overlapped_footprints.rds")
#asked for overlapped footprints that overlaps with peaks
list1 <- get_related_genes(footprints=overlapped,txdb=TxDb.Hsapiens.UCSC.hg38.knownGene,motif=Tranfac201803_Hs_MotifTFsF,Species = 'Hs')
list2<-get_related_peaks(list1,test_clustering)
list2
set parameter 'workers' to make this function run in parallel
cuts1 <- cal_footprint_cuts(bamfilepath = bamfilepath1,index_bam = FALSE, bedfile = list2[[1]],workers = 16)
##########################################################################
################################ Error #####################################
'select()' returned 1:many mapping between keys and columns
Error in checkForRemoteErrors(val) :
6 nodes produced errors; first error: replacement has length zero
Calls: cal_footprint_cuts ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Execution halted
############################## output #####################################
sequence_name start stop strand p.value matched_sequence motif_id
1 chr1 1906463 1906477 + 2.57e-05 AGTGCAGATGGGCTG M00002
2 chr1 3772662 3772676 - 8.95e-05 CCGGAAGGTGGCGGG M00002
3 chr1 3772678 3772692 - 9.15e-05 CGGGGAGGTGTCTGG M00002
4 chr1 6236008 6236022 - 9.63e-05 CGGGCAGCTGCCCTT M00002
5 chr1 6236009 6236023 + 6.29e-05 AGGGCAGCTGCCCGC M00002
6 chr1 11273438 11273452 - 9.65e-05 GGGGCAGCAGGGCCC M00002
[[2]]
V3 V4 V5 PeakGene V7 V8
228 chr1 100132937 100132948 ENSG00000156876|Promoter 100132882 100133002
229 chr1 100132937 100132952 ENSG00000156876|Promoter 100132864 100133024
230 chr1 100132937 100132954 ENSG00000156876|Promoter 100132855 100133035
231 chr1 100132937 100132958 ENSG00000156876|Promoter 100132837 100133057
232 chr1 100132938 100132955 ENSG00000156876|Promoter 100132856 100133036
233 chr1 100132938 100132958 ENSG00000156876|Promoter 100132843 100133053
234 chr1 100132938 100132959 ENSG00000156876|Promoter 100132838 100133058
235 chr1 100132939 100132950 ENSG00000156876|Promoter 100132884 100133004
236 chr1 100132939 100132960 ENSG00000156876|Promoter 100132839 100133059
237 chr1 100132940 100132957 ENSG00000156876|Promoter 100132858 100133038
238 chr1 100132940 100132959 ENSG00000156876|Promoter 100132849 100133049
239 chr1 100132940 100132961 ENSG00000156876|Promoter 100132840 100133060
240 chr1 100132941 100132954 ENSG00000156876|Promoter 100132877 100133017
241 chr1 100132941 100132956 ENSG00000156876|Promoter 100132868 100133028
242 chr1 100132944 100132965 ENSG00000156876|Promoter 100132844 100133064
243 chr1 100132946 100132967 ENSG00000156876|Promoter 100132846 100133066
244 chr1 100132948 100132958 ENSG00000156876|Promoter 100132898 100133008
245 chr1 100132948 100132959 ENSG00000156876|Promoter 100132893 100133013
246 chr1 100132948 100132960 ENSG00000156876|Promoter 100132889 100133019
247 chr1 100132948 100132960 ENSG00000156876|Promoter 100132889 100133019
.
.
.
23653 chr1 151909442 151909463 ENSG00000159445|Promoter 151909342 151909562
23654 chr1 151909444 151909450 ENSG00000159445|Promoter 151909412 151909482
23655 chr1 151909449 151909459 ENSG00000159445|Promoter 151909399 151909509
23656 chr1 151909449 151909460 ENSG00000159445|Promoter 151909394 151909514
23657 chr1 151909450 151909456 ENSG00000159445|Promoter 151909418 151909488
23658 chr1 151909450 151909470 ENSG00000159445|Promoter 151909355 151909565
23659 chr1 151909452 151909463 ENSG00000159445|Promoter 151909397 151909517
23660 chr1 151909453 151909468 ENSG00000159445|Promoter 151909380 151909540
23661 chr1 151909454 151909475 ENSG00000159445|Promoter 151909354 151909574
23662 chr1 151909455 151909466 ENSG00000159445|Promoter 151909400 151909520
23663 chr1 151909455 151909469 ENSG00000159445|Promoter 151909387 151909537
23664 chr1 151909456 151909469 ENSG00000159445|Promoter 151909392 151909532
23665 chr1 151909456 151909479 ENSG00000159445|Promoter 151909347 151909587
23666 chr1 151909457 151909469 ENSG00000159445|Promoter 151909398 151909528
23667 chr1 151909457 151909470 ENSG00000159445|Promoter 151909393 151909533
V9
228 M05891;ENSG00000197343
229 M09727;ENSG00000064703
230 M06193;ENSG00000152926
231 M09984;ENSG00000103495
232 M06193;ENSG00000152926
233 M07141;ENSG00000006194
234 M09984;ENSG00000103495
235 M06172;ENSG00000184939;ENSG00000 213988|M06223;ENSG00000204920|M06609;ENSG00000187626
236
.
.
.
M10375;ENSG00000185591
23666 M10176;ENSG00000087510
23667 M09591;ENSG00000087510
[ reached 'max' / getOption("max.print") -- omitted 900857 rows ]