Question

Question on bgzf_read error

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Kath • 0

@kath-18711

Last seen 5.1 years ago

Dear support,

I got an bgzf_read error while running diffbind dba.count(). I had posted the message here for the reference, could anyone kindly provide any advises? Thank you in advance!

https://www.biostars.org/p/406660/#407539

diffbind • 1.4k views

ADD COMMENT • link 5.1 years ago Kath • 0

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Hi,

Tagging your question with "software error" is not going to help you. Also you didn't provide your sessionInfo() or a reproducible example as required in our Posting Guide. Please make sure to read the Posting Guide if you want to be helped.

Thanks, H.

ADD REPLY • link 5.1 years ago Hervé Pagès 16k

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Thanks and here is the sessionInfo()

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DiffBind_2.12.0             SummarizedExperiment_1.14.1 DelayedArray_0.10.0         BiocParallel_1.18.1         matrixStats_0.54.0         
 [6] Biobase_2.44.0              GenomicRanges_1.36.0        GenomeInfoDb_1.20.0         IRanges_2.18.2              S4Vectors_0.22.0           
[11] BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] Category_2.50.0          bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2       progress_1.2.2          
 [6] httr_1.4.1               Rgraphviz_2.28.0         tools_3.6.1              backports_1.1.4          R6_2.4.0                
[11] KernSmooth_2.23-15       DBI_1.0.0                lazyeval_0.2.2           colorspace_1.4-1         withr_2.1.2             
[16] tidyselect_0.2.5         prettyunits_1.0.2        bit_1.1-14               compiler_3.6.1           graph_1.62.0            
[21] rtracklayer_1.44.4       checkmate_1.9.4          caTools_1.17.1.2         scales_1.0.0             genefilter_1.66.0       
[26] RBGL_1.60.0              rappdirs_0.3.1           stringr_1.4.0            digest_0.6.20            Rsamtools_2.0.2         
[31] AnnotationForge_1.26.0   XVector_0.24.0           pkgconfig_2.0.2          BSgenome_1.52.0          limma_3.40.6            
[36] rlang_0.4.0              rstudioapi_0.10          RSQLite_2.1.2            GOstats_2.50.0           hwriter_1.3.2           
[41] gtools_3.8.1             dplyr_0.8.3              VariantAnnotation_1.30.1 RCurl_1.95-4.12          magrittr_1.5            
[46] GO.db_3.8.2              GenomeInfoDbData_1.2.1   Matrix_1.2-17            Rcpp_1.0.2               munsell_0.5.0           
[51] stringi_1.4.3            yaml_2.2.0               edgeR_3.26.8             zlibbioc_1.30.0          gplots_3.0.1.1          
[56] grid_3.6.1               blob_1.2.0               ggrepel_0.8.1            gdata_2.18.0             crayon_1.3.4            
[61] lattice_0.20-38          Biostrings_2.52.0        splines_3.6.1            GenomicFeatures_1.36.4   annotate_1.62.0         
[66] hms_0.5.1                batchtools_0.9.11        locfit_1.5-9.1           zeallot_0.1.0            pillar_1.4.2            
[71] rjson_0.2.20             systemPipeR_1.18.2       base64url_1.4            biomaRt_2.40.4           XML_3.98-1.20           
[76] glue_1.3.1               ShortRead_1.42.0         latticeExtra_0.6-28      data.table_1.12.2        vctrs_0.2.0             
[81] gtable_0.3.0             purrr_0.3.2              amap_0.8-17              assertthat_0.2.1         ggplot2_3.2.1           
[86] xtable_1.8-4             survival_2.44-1.1        pheatmap_1.0.12          tibble_2.1.3             GenomicAlignments_1.20.1
[91] AnnotationDbi_1.46.1     memoise_1.1.0            brew_1.0-6               GSEABase_1.46.0

ADD REPLY • link updated 5.1 years ago by Martin Morgan 25k • written 5.1 years ago by Kath • 0

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Good thanks! By having tagged your question with the name of the package you are using you're getting a lot more chance to receive attention and help from the right people. They might still need a reproducible example (a.k.a. "minimal working example" or MWE) in order to be able to help but that's up to them.

ADD REPLY • link 5.1 years ago Hervé Pagès 16k

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How large are the files? Can you try on a non-Windows operating system?

ADD REPLY • link 5.1 years ago Martin Morgan 25k

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The largest bam is around 2gb. I haven't try mac/linux system yet for diffbind, do you think it's might be due to the platform issue? I can try rstudio at linux and see how it goes then

ADD REPLY • link 5.1 years ago Kath • 0

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My guess would be an integer overflow on Windows, the critical size is 'around' 2Gb, specifically

> .Machine$integer.max
[1] 2147483647

would you be willing to share the problem file?

ADD REPLY • link 5.1 years ago Martin Morgan 25k

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Thank you! I did try win-based VM linux, and there was no error out while running dba.count(). However, when I plotted the sample correlation in the next step, it's the same plot with those 4 blank samples. It looked that those 4 samples still not readin with dba.count().

I can share those files, where to share?

ADD REPLY • link 5.1 years ago Kath • 0

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The update --

I re-run diffbind at linux server instead of the VM, those files processed successfully. It seems that the VM has the same limitation as the windows.

Thank you very much for the comment!

ADD REPLY • link 5.1 years ago Kath • 0