Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R

[chrisodhams]

Hi,

Not sure if this is the same error as #395 - which requires internet connection.

Note that I am not possible to get internet connection as I am working from a secure research environment with no inbound internet connection.

See the log attached.
log.txt

There seems to be an error showing:

Mon Apr 17 14:19:10 2023: Count split reads for sample: LP5001322-RNA_E02 Error in asMethod(object) : The character vector to convert to a GRanges object must contain strings of the form "chr:start-end" or "chr:start-end:strand", with end >= start - 1, or "chr:pos" or "chr:pos:strand". For example: "chr1:2501-2900", "chr1:2501-2900:+", or "chr1:740". Note that ".." is a valid alternate start/end separator. Strand can be "+", "-", " *", or missing. Calls: countSplitReads -> GRanges -> as -> asMethod Execution halted

[ischeller]

The step that would require internet connection in the counting script is the obtaining the list of standard chromosomes to which we subset when using the default parameters. So if you set
keepNonStandardChrs: true in the config.yaml, you should be able to avoid errors related to that (see https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#aberrant-splicing-dictionary).

However, given the error message you receive, the issue might be something else here. Could you check what output you get when you run the following lines in R?
library(FRASER)
fds <- loadFraserDataSet(file='/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets//savedObjects/raw-local-group1/fds-object.RDS')
FRASER:::extractChromosomes(bamFile(fds[,"LP5001322-RNA_E02"]))

[chrisodhams]

Hi @ischeller ,
Thank you. Please see the output attached. Could it be due to * chars in chromosome names for the HLA contigs such as HLA-C*07:385
output.txt
Best,
Chris

[vyepez88]

Hi @chrisodhams, yes, that * or the : could be the culprit. Setting keepNonStandardChrs: true might fix it.

[vyepez88]

We found a fix. @ischeller is working on it.

[ischeller]

Hi @chrisodhams ,
as @vyepez88 suggested, when running DROP with keepNonStandardChrs: true , you should not run into this issue in the first place.
For the error you got, the contig names were indeed the issue. We fixed this in FRASER 1.99.3, so you could reinstall FRASER with BiocManager::install("gagneurlab/FRASER"). However, given that you want to run without internet connection , just setting keepNonStandardChrs: true should be enough in your case already.

[chrisodhams]

Hi @vyepez88 @ischeller ,
Many thanks - will try this suggestion and let you know.
Best,