roleren / uorfomepipe Goto Github PK

The code I run:
df.rfp <- read.experiment("Abby_Mouse_Ribo-seq")
df.rna <- read.experiment("Abby_Mouse_RNA-seq")
find_uORFome("/n/jobspace/bbcore/schaffer_rpf_abby_min6/two_batches/uORFome", organism = "Mus musculus",
df.rfp = df.rfp, df.rna = df.rna, df.cage = NULL, biomart = NULL)

The error message:

Making training data from CDS and trailers (3' UTRs):

Finding Ribo-seq features for cds
/n/jobspace/bbcore/schaffer_rpf_abby_min6/two_batches/bam/rpf/pshifted/20210125_Index_1_JS8600_S9_R1_001_UMIremoved_pshifted.ofst
Error: BiocParallel errors
1 remote errors, element index: 1
15 unevaluated and other errors
first remote error:
Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlengths of x contains NA values!

hello again,
thanks for your help in ORFik, I met another problem in the final step of ...uORF analysis... .

When I run :

find_uORFome("/home/bio/biosoft/riboseq_data/projects/Alexaki_uORFome/",organism = "Homo sapiens",
             df.rfp = df.rfp, df.rna = df.rna, df.cage = NULL, biomart = NULL,
             startCodons = "ATG|CTG|TTG|GTG", BPPARAM = BiocParallel::MulticoreParam())

I got the error

useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

after checking, I found it was due to the function createCatalogueDB.

createCatalogueDB(df.cage)
uniqueIDs already exist, skipping remake of them
Creating GRanges objects
Creating merged leader
错误: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

the version of uORFomePipe is 0.2.1.

do you have any suggestions ？

sincerely !