Question

Importing transcript abundance datasets generated with Salmon 0.14.0

0

Entering edit mode

edoardobertolini • 0

@edoardobertolini-15135

Last seen 3.1 years ago

United States

Hi! I have recently updated Salmon to the latest version (0.14.0) and I'm not anymore able to import Salmon outputs into R using the code

tximport(file, type = "salmon", txOut = TRUE, countsFromAbundance = "no")

This is the error that I get when I run the code above:

txi <- tximport(file, type = "salmon", txOut = TRUE, countsFromAbundance = "no") reading in files with read_tsv Error in readBin(bootCon, "integer", n = expected.n) : invalid 'n' argument

Any suggestion? Thanks

Edo

tximport • 1.1k views

ADD COMMENT • link updated 5.5 years ago by Michael Love 43k • written 5.5 years ago by edoardobertolini • 0

score 0 · Answer 1 · 2019-06-10

0

Entering edit mode

Michael Love 43k

@mikelove

Last seen 2 days ago

United States

This was just fixed by Rory Kirchner, and we will propagate to release (1.12.1) and devel (1.13.3).

ADD COMMENT • link 5.5 years ago Michael Love 43k

0

Entering edit mode

Getting the same error, is there any quick fix? Thanks ML for working on it.

ADD REPLY • link 5.5 years ago drowsygoat ▴ 30

0

Entering edit mode

It's fixed. What version are you using?

sessionInfo()

ADD REPLY • link 5.5 years ago Michael Love 43k

0

Entering edit mode

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] tximport_1.13.3      biomaRt_2.41.3       matrixStats_0.54.0   data.table_1.12.2    pheatmap_1.0.12     
 [6] org.Mm.eg.db_3.8.2   AnnotationDbi_1.47.0 IRanges_2.19.9       S4Vectors_0.23.11    Biobase_2.45.0      
[11] BiocGenerics_0.31.4 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.15.1 progress_1.2.2              tidyselect_0.2.5           
 [4] purrr_0.3.2                 rhdf5_2.29.0                lattice_0.20-38            
 [7] colorspace_1.4-1            blob_1.1.1                  XML_3.98-1.20              
[10] rlang_0.3.4                 pillar_1.4.1                glue_1.3.1                 
[13] DBI_1.0.0                   BiocParallel_1.19.0         bit64_0.9-7                
[16] RColorBrewer_1.1-2          GenomeInfoDbData_1.2.1      stringr_1.4.0              
[19] zlibbioc_1.31.0             munsell_0.5.0               gtable_0.3.0               
[22] memoise_1.1.0               GenomeInfoDb_1.21.1         curl_3.3                   
[25] Rcpp_1.0.1                  readr_1.3.1                 scales_1.0.0               
[28] BiocManager_1.30.4          DelayedArray_0.11.0         jsonlite_1.6               
[31] XVector_0.25.0              bit_1.1-14                  hms_0.4.2                  
[34] digest_0.6.19               stringi_1.4.3               dplyr_0.8.1                
[37] GenomicRanges_1.37.10       grid_3.6.0                  tools_3.6.0                
[40] bitops_1.0-6                magrittr_1.5                RCurl_1.95-4.12            
[43] RSQLite_2.1.1               tibble_2.1.3                crayon_1.3.4               
[46] pkgconfig_2.0.2             Matrix_1.2-17               prettyunits_1.0.2          
[49] assertthat_0.2.1            httr_1.4.0                  rstudioapi_0.10            
[52] Rhdf5lib_1.7.2              R6_2.4.0                    compiler_3.6.0

ADD REPLY • link 5.5 years ago drowsygoat ▴ 30

1

Entering edit mode

Can you reload R and try the code again?

At least two others have reported that the new versions fix the bug.

ADD REPLY • link 5.5 years ago Michael Love 43k

1

Entering edit mode

OK, I reinstalled it and now it's working! Thanks again Michael!

ADD REPLY • link 5.5 years ago drowsygoat ▴ 30