Question: Question on bgzf_read error
0
gravatar for Kath
4 weeks ago by
Kath0
Kath0 wrote:

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 • 85 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Kath0

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 REPLYlink written 4 weeks ago by Hervé Pagès ♦♦ 14k

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 REPLYlink written 4 weeks ago by Kath0

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 REPLYlink written 4 weeks ago by Hervé Pagès ♦♦ 14k

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

ADD REPLYlink written 4 weeks ago by Martin Morgan ♦♦ 24k

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 REPLYlink written 4 weeks ago by Kath0

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 REPLYlink written 4 weeks ago by Martin Morgan ♦♦ 24k

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 REPLYlink modified 4 weeks ago • written 4 weeks ago by Kath0

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 REPLYlink written 25 days ago by Kath0
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