Hi, I'm trying to calculate tumor purity and ploidy using a tool called PureCN written in Rscript. The initial step is to generate an interval file based on GC content from hg38.bed and hg38.fa files. The command used for the process is given below: Rscript $PURECN/IntervalFile.R --infile /path/to/hg19.bed --fasta /path/to/hg19.fa --outfile /path/to/hg19_intervals.txt
The following error shows up:
Error in value[3L] : record 4423505 (chr1_KN196472v1_fix:111333-111727) failed file: /path/to/hg38.fa Calls: preprocessIntervals ... tryCatch -> tryCatchList -> tryCatchOne -> <anonymous>
It would be of great help if someone could help me out in troubleshooting this error. Thanks in advance.