Estimados, espero se encuentre bien. He estado teniendo un problema recurrente con ASpli que no he sabido solucionar.
Había estado analizando muchas librerias sin problemas, pero en tres ocasiones he tenido problemas con este mismo error cuando esta corriendo la funcion JCounts
El error:
asd <- jCounts(counts=gbcounts, features=features, minReadLength=18, libType="SE", strandMode=2)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a methError ASpli.txtod for function 'sort': 'start' or 'end' cannot contain NAs
In addition: Warning messages:
1: In matrix(unlist(strsplit(jnames, "[.]")), byrow = TRUE, ncol = 3) :
data length [422626] is not a sub-multiple or multiple of the number of rows [140876]
2: In .createGRangesExpJunctions(junctionNames) :
NAs introduced by coercion
Cosas que he intentado (solo para probar):
-Cambiar el libtype y strandmode
-He rehecho los BAMs e incluso los SAMs
-Reanalicé utilizando otro programa de trimming. Antes estaba usando Trimgalore y pase a Trimmomatic. Trimmomatic me solucionó el problema para algunos datasets, pero hay estos tres en especifico que me siguen dando ese mismo error. Uno de ellos me interesa mucho porque es de los pocos que hay con raiz de arabidopsis en estres salino.
Dejo las accession numbers y mi sessioninfo.
######Input
BAMFiles <- c("Control_1.bam","Control_2.bam", "NaCl_1.bam", "NaCl_2.bam")
targets <- data.frame(row.names = paste0('Sample',c(1:4)),
bam = BAMFiles[1:4],
f1 = c( 'control','control','control','treatment','treatment'),
stringsAsFactors = FALSE); targets
mBAMs <- data.frame( bam = c("Control_sorted.bam", "NaCl_sorted.bam"),
condition = c("control","treatment")); mBAMs
gbcounts <- gbCounts(features=features, targets=targets, minReadLength = 18, maxISize = 50000, libType="SE", strandMode=1)
asd <- jCounts(counts=gbcounts, features=features, minReadLength=18, libType="SE", strandMode=1) #stranded
gb <- gbDUreport(gbcounts, contrast = c(-1,1))
jdur <- jDUreport(asd, contrast=c(-1,1))
sr <- splicingReport(gb, jdur, counts=gbcounts)
is <- integrateSignals(sr,asd, bin.FC=1)
exportSplicingReports(sr, output.dir="19.sr")
exportIntegratedSignals(is,sr=sr, output.dir = "19.SplicingReport", counts=gbcounts,features=features,asd=asd, mergedBams = mBAMs)
#######Accession numbers
SRR8424695 Control_1
SRR8424694 Control_2
SRR8424692 NaCl_1
SRR8424691 NaCl_2
#######My sessioninfo
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /home/jesusm/anaconda3/envs/env1/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] statmod_1.4.37 GenomicFeatures_1.50.2 GenomicRanges_1.50.0
[4] GenomeInfoDb_1.34.1 ASpli_2.8.0 AnnotationDbi_1.60.0
[7] IRanges_2.32.0 S4Vectors_0.36.0 Biobase_2.58.0
[10] BiocGenerics_0.44.0 edgeR_3.40.0 limma_3.54.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 rjson_0.2.21
[3] deldir_1.0-6 ellipsis_0.3.2
[5] biovizBase_1.46.0 htmlTable_2.4.1
[7] XVector_0.38.0 base64enc_0.1-3
[9] dichromat_2.0-0.1 rstudioapi_0.14
[11] DT_0.26 bit64_4.0.5
[13] fansi_1.0.3 xml2_1.3.3
[15] codetools_0.2-18 splines_4.2.2
[17] cachem_1.0.6 knitr_1.41
[19] Formula_1.2-4 Rsamtools_2.14.0
[21] cluster_2.1.4 dbplyr_2.2.1
[23] png_0.1-8 BiocManager_1.30.19
[25] compiler_4.2.2 httr_1.4.4
[27] backports_1.4.1 lazyeval_0.2.2
[29] assertthat_0.2.1 Matrix_1.5-3
[31] fastmap_1.1.0 cli_3.5.0
[33] htmltools_0.5.4 prettyunits_1.1.1
[35] tools_4.2.2 igraph_1.3.5
[37] gtable_0.3.1 glue_1.6.2
[39] GenomeInfoDbData_1.2.9 dplyr_1.0.10
[41] rappdirs_0.3.3 Rcpp_1.0.9
[43] vctrs_0.5.1 Biostrings_2.66.0
[45] rtracklayer_1.58.0 xfun_0.36
[47] stringr_1.5.0 lifecycle_1.0.3
[49] ensembldb_2.22.0 restfulr_0.0.15
[51] XML_3.99-0.13 zlibbioc_1.44.0
[53] MASS_7.3-58.1 scales_1.2.1
[55] BiocStyle_2.26.0 BSgenome_1.66.1
[57] VariantAnnotation_1.44.0 ProtGenerics_1.30.0
[59] hms_1.1.2 MatrixGenerics_1.10.0
[61] SummarizedExperiment_1.28.0 AnnotationFilter_1.22.0
[63] RColorBrewer_1.1-3 yaml_2.3.6
[65] curl_4.3.3 memoise_2.0.1
[67] gridExtra_2.3 ggplot2_3.4.0
[69] UpSetR_1.4.0 biomaRt_2.54.0
[71] rpart_4.1.19 latticeExtra_0.6-30
[73] stringi_1.7.8 RSQLite_2.2.20
[75] BiocIO_1.8.0 checkmate_2.1.0
[77] filelock_1.0.2 BiocParallel_1.32.0
[79] rlang_1.0.6 pkgconfig_2.0.3
[81] matrixStats_0.63.0 bitops_1.0-7
[83] evaluate_0.19 lattice_0.20-45
[85] purrr_1.0.0 htmlwidgets_1.6.0
[87] GenomicAlignments_1.34.0 bit_4.0.5
[89] tidyselect_1.2.0 plyr_1.8.8
[91] magrittr_2.0.3 R6_2.5.1
[93] generics_0.1.3 Hmisc_4.7-2
[95] DelayedArray_0.24.0 DBI_1.1.3
[97] pillar_1.8.1 foreign_0.8-84
[99] survival_3.4-0 KEGGREST_1.38.0
[101] RCurl_1.98-1.9 nnet_7.3-18
[103] tibble_3.1.8 crayon_1.5.2
[105] interp_1.1-3 utf8_1.2.2
[107] BiocFileCache_2.6.0 rmarkdown_2.19
[109] jpeg_0.1-10 progress_1.2.2
[111] locfit_1.5-9.6 grid_4.2.2
[113] data.table_1.14.6 blob_1.2.3
[115] digest_0.6.31 pbmcapply_1.5.1
[117] tidyr_1.2.1 munsell_0.5.0
[119] Gviz_1.42.0
Saludos!
Error ASpli.txt
Estimados, espero se encuentre bien. He estado teniendo un problema recurrente con ASpli que no he sabido solucionar.
Había estado analizando muchas librerias sin problemas, pero en tres ocasiones he tenido problemas con este mismo error cuando esta corriendo la funcion JCounts
El error:
Cosas que he intentado (solo para probar):
-Cambiar el libtype y strandmode
-He rehecho los BAMs e incluso los SAMs
-Reanalicé utilizando otro programa de trimming. Antes estaba usando Trimgalore y pase a Trimmomatic. Trimmomatic me solucionó el problema para algunos datasets, pero hay estos tres en especifico que me siguen dando ese mismo error. Uno de ellos me interesa mucho porque es de los pocos que hay con raiz de arabidopsis en estres salino.
Dejo las accession numbers y mi sessioninfo.
######Input
BAMFiles <- c("Control_1.bam","Control_2.bam", "NaCl_1.bam", "NaCl_2.bam")
targets <- data.frame(row.names = paste0('Sample',c(1:4)),
bam = BAMFiles[1:4],
f1 = c( 'control','control','control','treatment','treatment'),
stringsAsFactors = FALSE); targets
mBAMs <- data.frame( bam = c("Control_sorted.bam", "NaCl_sorted.bam"),
condition = c("control","treatment")); mBAMs
gbcounts <- gbCounts(features=features, targets=targets, minReadLength = 18, maxISize = 50000, libType="SE", strandMode=1)
asd <- jCounts(counts=gbcounts, features=features, minReadLength=18, libType="SE", strandMode=1) #stranded
gb <- gbDUreport(gbcounts, contrast = c(-1,1))
jdur <- jDUreport(asd, contrast=c(-1,1))
sr <- splicingReport(gb, jdur, counts=gbcounts)
is <- integrateSignals(sr,asd, bin.FC=1)
exportSplicingReports(sr, output.dir="19.sr")
exportIntegratedSignals(is,sr=sr, output.dir = "19.SplicingReport", counts=gbcounts,features=features,asd=asd, mergedBams = mBAMs)
#######Accession numbers
SRR8424695 Control_1
SRR8424694 Control_2
SRR8424692 NaCl_1
SRR8424691 NaCl_2
#######My sessioninfo
Matrix products: default
BLAS/LAPACK: /home/jesusm/anaconda3/envs/env1/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] statmod_1.4.37 GenomicFeatures_1.50.2 GenomicRanges_1.50.0
[4] GenomeInfoDb_1.34.1 ASpli_2.8.0 AnnotationDbi_1.60.0
[7] IRanges_2.32.0 S4Vectors_0.36.0 Biobase_2.58.0
[10] BiocGenerics_0.44.0 edgeR_3.40.0 limma_3.54.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 rjson_0.2.21
[3] deldir_1.0-6 ellipsis_0.3.2
[5] biovizBase_1.46.0 htmlTable_2.4.1
[7] XVector_0.38.0 base64enc_0.1-3
[9] dichromat_2.0-0.1 rstudioapi_0.14
[11] DT_0.26 bit64_4.0.5
[13] fansi_1.0.3 xml2_1.3.3
[15] codetools_0.2-18 splines_4.2.2
[17] cachem_1.0.6 knitr_1.41
[19] Formula_1.2-4 Rsamtools_2.14.0
[21] cluster_2.1.4 dbplyr_2.2.1
[23] png_0.1-8 BiocManager_1.30.19
[25] compiler_4.2.2 httr_1.4.4
[27] backports_1.4.1 lazyeval_0.2.2
[29] assertthat_0.2.1 Matrix_1.5-3
[31] fastmap_1.1.0 cli_3.5.0
[33] htmltools_0.5.4 prettyunits_1.1.1
[35] tools_4.2.2 igraph_1.3.5
[37] gtable_0.3.1 glue_1.6.2
[39] GenomeInfoDbData_1.2.9 dplyr_1.0.10
[41] rappdirs_0.3.3 Rcpp_1.0.9
[43] vctrs_0.5.1 Biostrings_2.66.0
[45] rtracklayer_1.58.0 xfun_0.36
[47] stringr_1.5.0 lifecycle_1.0.3
[49] ensembldb_2.22.0 restfulr_0.0.15
[51] XML_3.99-0.13 zlibbioc_1.44.0
[53] MASS_7.3-58.1 scales_1.2.1
[55] BiocStyle_2.26.0 BSgenome_1.66.1
[57] VariantAnnotation_1.44.0 ProtGenerics_1.30.0
[59] hms_1.1.2 MatrixGenerics_1.10.0
[61] SummarizedExperiment_1.28.0 AnnotationFilter_1.22.0
[63] RColorBrewer_1.1-3 yaml_2.3.6
[65] curl_4.3.3 memoise_2.0.1
[67] gridExtra_2.3 ggplot2_3.4.0
[69] UpSetR_1.4.0 biomaRt_2.54.0
[71] rpart_4.1.19 latticeExtra_0.6-30
[73] stringi_1.7.8 RSQLite_2.2.20
[75] BiocIO_1.8.0 checkmate_2.1.0
[77] filelock_1.0.2 BiocParallel_1.32.0
[79] rlang_1.0.6 pkgconfig_2.0.3
[81] matrixStats_0.63.0 bitops_1.0-7
[83] evaluate_0.19 lattice_0.20-45
[85] purrr_1.0.0 htmlwidgets_1.6.0
[87] GenomicAlignments_1.34.0 bit_4.0.5
[89] tidyselect_1.2.0 plyr_1.8.8
[91] magrittr_2.0.3 R6_2.5.1
[93] generics_0.1.3 Hmisc_4.7-2
[95] DelayedArray_0.24.0 DBI_1.1.3
[97] pillar_1.8.1 foreign_0.8-84
[99] survival_3.4-0 KEGGREST_1.38.0
[101] RCurl_1.98-1.9 nnet_7.3-18
[103] tibble_3.1.8 crayon_1.5.2
[105] interp_1.1-3 utf8_1.2.2
[107] BiocFileCache_2.6.0 rmarkdown_2.19
[109] jpeg_0.1-10 progress_1.2.2
[111] locfit_1.5-9.6 grid_4.2.2
[113] data.table_1.14.6 blob_1.2.3
[115] digest_0.6.31 pbmcapply_1.5.1
[117] tidyr_1.2.1 munsell_0.5.0
[119] Gviz_1.42.0
Saludos!
Error ASpli.txt