Error in base::basename(path, ...) : a character vector argument expected

[deb0612]

Dear sir: I tried data =superFreq(file, normalDirectory=normalDirectory, Rdirectory=Rdirectory, plotDirectory=plotDirectory, reference=reference, genome=genome, cpus=cpus, mode=mode) But I got error below: runtimeTracking.log

Normal directory: /NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RSEM/referenceNormals Normal coverage directory: /NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RSEM/referenceNormals dbSNP directory: superFreqResources/dbSNP capture regions: will be downloaded from superFreq server. Plotting to /NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RSEM/plots/RNA-leukemia002A Saving R files to /NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RSEM/R/RNA-leukemia002A Genome is hg38 Running in RNA mode. exacPopulation is all Running on at most 4 cpus. Rare germline variants are shown in output.

Parameters for this run are: maxCov: 150 systematicVariance: 0.03 cloneDistanceCut: 2.326348 cosmicSalvageRate: 0.001

Error in base::basename(path, ...) : a character vector argument expected

[ChristofferFlensburg]

Hey!

That part is where the reference normal BAM files are identified. I think it doesn't find any BAM files. I really thought it'd make a more informative error message if it didn't find any bams, so seems I need to look into and probably fix that.

SuperFreq expects the reference normal BAM files (and .bai index files) to be (linked) in the a subdirectory called bam in the reference normal directory. It also looks in top level of reference normal directory just in case. So that'd be NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RSEM/referenceNormals/bam and NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RSEM/referenceNormals in your case. I think SuperFreq didnt find any BAM files there, which caused the crash.

Let me know if that solves it.