JesusMHU
commented
1 year ago Otra info: -He hecho todos los analisis con la misma anotación. -Probé la devel version de ASpli 2.9 y aun me sale el error con estas librerias -He intentado cambiar el strandmode a unstranded, forward stranded y reverse stranded y genera el mismo error. -Mi read length es de 18. Probe cambiarlo a 50 y aun genera el mismo error. -Samtools view de dos de los BAMs problematicos:
(env1) jesusm@LAPTOP-S6C7NUN7:/mnt/e/WDSS/(19) PRJNA514040 - SE$ samtools view -H NaCl_1.bam @HD VN:1.0 SO:unsorted @SQ SN:Chr1 LN:30427671 @SQ SN:Chr2 LN:19698289 @SQ SN:Chr3 LN:23459830 @SQ SN:Chr4 LN:18585056 @SQ SN:Chr5 LN:26975502 @SQ SN:ChrC LN:154478 @SQ SN:ChrM LN:367808 @PG ID:hisat2 PN:hisat2 VN:2.1.0 CL:"/mnt/e/WDSS/tools/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 --rna-strandness F -x /mnt/e/WDSS/TAIR10_Chr.all -S SRR8424692.fastq.gz.trim.fil.gz.sam -U /tmp/1818.unp"
(env1) jesusm@LAPTOP-S6C7NUN7:/mnt/e/WDSS/(19) PRJNA514040 - SE$ samtools view -H Control_1.bam @HD VN:1.0 SO:unsorted @SQ SN:Chr1 LN:30427671 @SQ SN:Chr2 LN:19698289 @SQ SN:Chr3 LN:23459830 @SQ SN:Chr4 LN:18585056 @SQ SN:Chr5 LN:26975502 @SQ SN:ChrC LN:154478 @SQ SN:ChrM LN:367808 @PG ID:hisat2 PN:hisat2 VN:2.1.0 CL:"/mnt/e/WDSS/tools/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 --rna-strandness F -x /mnt/e/WDSS/TAIR10_Chr.all -S SRR8424695.fastq.gz.trim.fil.gz.sam -U /tmp/1859.unp"
estepi
rfarouni
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