Hello all,

I'm running ASpli package for alternative splicing analysis in a plant called Glycine max and i'm having the issue of a never ending process when the pipeline reaches the counting step. I let it run for 30 hours in a virtual machine on google of 24CPUs and 150GB RAM, but it never got me any result, so i killed the process. It used around 92GB RAM in the counting step and never ends. I used the 'toy' dataset to test the installation, dependencies and pipeline, and it went great, with no errors.

Whats could be the problem?

Some important info:

The point it gets stuck and never results in anything:

> counts <- readCounts(features=features, bam=bam, targets=targets, cores=20, readLength=100L, maxISize=50000, minAnchor=10)
Read summarization by gene completed
Read summarization by bin completed
Read summarization by ei1 region completed
Read summarization by ie2 region completed

Information about the R session:

 > sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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] GenomicFeatures_1.34.3 AnnotationDbi_1.44.0   Biobase_2.42.0        
 [4] GenomicRanges_1.34.0   GenomeInfoDb_1.18.1    IRanges_2.16.0        
 [7] S4Vectors_0.20.1       BiocGenerics_0.28.0    ASpli_1.8.1           
[10] edgeR_3.24.3           limma_3.38.3          

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.14.0         bitops_1.0-6               
 [3] matrixStats_0.54.0          bit64_0.9-7                
 [5] RColorBrewer_1.1-2          progress_1.2.0             
 [7] httr_1.4.0                  tools_3.5.2                
 [9] backports_1.1.3             R6_2.3.0                   
[11] rpart_4.1-13                Hmisc_4.2-0                
[13] DBI_1.0.0                   lazyeval_0.2.1             
[15] Gviz_1.26.4                 colorspace_1.4-0           
[17] nnet_7.3-12                 gridExtra_2.3              
[19] prettyunits_1.0.2           bit_1.1-14                 
[21] curl_3.3                    compiler_3.5.2             
[23] htmlTable_1.13.1            DelayedArray_0.8.0         
[25] rtracklayer_1.42.1          scales_1.0.0               
[27] checkmate_1.9.1             stringr_1.4.0              
[29] digest_0.6.18               Rsamtools_1.34.1           
[31] foreign_0.8-70              rmarkdown_1.11             
[33] XVector_0.22.0              base64enc_0.1-3            
[35] dichromat_2.0-0             pkgconfig_2.0.2            
[37] htmltools_0.3.6             ensembldb_2.6.5            
[39] BSgenome_1.50.0             htmlwidgets_1.3            
[41] rlang_0.3.1                 rstudioapi_0.9.0           
[43] RSQLite_2.1.1               BiocParallel_1.16.5        
[45] acepack_1.4.1               VariantAnnotation_1.28.10  
[47] RCurl_1.95-4.11             magrittr_1.5               
[49] GenomeInfoDbData_1.2.0      Formula_1.2-3              
[51] Matrix_1.2-15               Rcpp_1.0.0                 
[53] munsell_0.5.0               stringi_1.2.4              
[55] yaml_2.2.0                  SummarizedExperiment_1.12.0
[57] zlibbioc_1.28.0             plyr_1.8.4                 
[59] grid_3.5.2                  blob_1.1.1                 
[61] crayon_1.3.4                lattice_0.20-38            
[63] Biostrings_2.50.2           splines_3.5.2              
[65] hms_0.4.2                   locfit_1.5-9.1             
[67] knitr_1.21                  pillar_1.3.1               
[69] biomaRt_2.38.0              XML_3.98-1.17              
[71] evaluate_0.12               biovizBase_1.30.1          
[73] latticeExtra_0.6-28         data.table_1.12.0          
[75] BiocManager_1.30.4          gtable_0.2.0               
[77] assertthat_0.2.0            ggplot2_3.1.0              
[79] xfun_0.4                    AnnotationFilter_1.6.0     
[81] survival_2.43-3             tibble_2.0.1               
[83] GenomicAlignments_1.18.1    memoise_1.1.0              
[85] cluster_2.0.7-1             BiocStyle_2.10.0

Reference data used from Phytozome: Gmax: Gmax275Wm82.a2.v1.gene.gff3.gz
Fasta file used to generate bam files, also from Phytozome: Gmax275v2.0.fa.gz (Data from this Phytozome link)

Any help or tip will be greatly appreciated!

Thank you all in advance.

Cordially,

Fernanda Costa