ORFikQC() error

[Braulium]

Dear ORFik team,

I am trying to use ORFik for analysing my Ribo-Seq experiments.

I create the experiment and everything seems to be working normal:

create.experiment(dir = dir,
                  rep = c(1,1,1,2,2,2),
                  saveDir = "~/Bio_data/ORFik_experiments/",
                  condition = c("38.7U", "200U", "400U", "38.7U", "200U", "400U"),
                  exper = "all_reads1",
                  txdb = "C:/Users/ortiz0000/Desktop/postdoc/common_resources/gencode.vM25.annotation.gtf",
                  fa = "C:/Users/ortiz0000/Desktop/postdoc/common_resources/GRCm38.primary_assembly.genome.fa",
                  organism = "Mus musculus",
                  assembly = "GRCm38",
                  pairedEndBam = FALSE,
                  viewTemplate = FALSE,
                  libtype = "Ribo-Seq",
                  stage = c("forebrain","forebrain","forebrain","forebrain","forebrain","forebrain"),
                  fraction = "RPF",
                  author = ""
)

df.rfp1 <- read.experiment("all_reads1")
df.rfp1

experiment: all_reads1 with 1 library type and 6 runs 
    libtype rep condition
1: Ribo-Seq   1     38.7U
2: Ribo-Seq   1      200U
3: Ribo-Seq   1      400U
4: Ribo-Seq   2     38.7U
5: Ribo-Seq   2      200U
6: Ribo-Seq   2      400U

but when I use ORFikQC(df.rfp1), I get:

Started ORFik QC report for experiment: all_reads1
Saving, ofst files to: C:/Users/ortiz0000/Desktop/postdoc/projects/eIF3g/Polysome profiling and Ribosome footprinting/Polysome profiling/2022-05-06 - B6 cortex tissue, cushion method/RiboSeq data analysis/5_umi_dedup_all_reads/ofst/
Outputting libraries from: all_reads1
5 :  Ribo-Seq_200U_r2

4 :  Ribo-Seq_38.7U_r2

6 :  Ribo-Seq_400U_r2

3 :  Ribo-Seq_400U_r1

2 :  Ribo-Seq_200U_r1

1 :  Ribo-Seq_38.7U_r1

--------------------------
Converting libraries to new format: ofst
Ribo-Seq_38.7U_r1
fstcore package v0.9.12
(OpenMP detected, using 8 threads)
Ribo-Seq_200U_r1
Ribo-Seq_400U_r1
Ribo-Seq_38.7U_r2
Ribo-Seq_200U_r2
Ribo-Seq_400U_r2
--------------------------
- Creating read length tables:
Using previously stored readlengths in QC_STATS folder!
--------------------------
- Creating read count tables for region:
cds
Loading existing count table, set forceRemake=TRUE if you want to remake

- Creating read count tables for region:
leaders
Loading existing count table, set forceRemake=TRUE if you want to remake

- Creating read count tables for region:
mrna
Loading existing count table, set forceRemake=TRUE if you want to remake

- Creating read count tables for region:
trailers
Loading existing count table, set forceRemake=TRUE if you want to remake

--------------------------
Making alignment statistics for lib:
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Ribo-Seq_200U_r2

Ribo-Seq_38.7U_r2

Ribo-Seq_400U_r1

Ribo-Seq_200U_r1

Ribo-Seq_38.7U_r1

Ribo-Seq_400U_r2

Error: BiocParallel errors
  6 remote errors, element index: 1, 2, 3, 4, 5, 6
  0 unevaluated and other errors
  first remote error:
Error in get(s): object 'Ribo-Seq_38.7U_r1' not found
In addition: There were 18 warnings (use warnings() to see them)

I don't understand why it cannot find Ribo-Seq_38.7U_r1 and the rest of the files, they are created and present in the global environment.

Thanks a lot and best regards, Raul

[Roleren]

It looks like you created the experiment correctly, so this might be a corner case bug, will do some tests and let you know tomorrow.

[Roleren]

Ah, yes I think I know what the error is, to verify it, can you please send me your output from these two calls: BiocParallel::registered() sessionInfo()