Closed NikdAK closed 3 years ago
"reduce_all_segments" (combining CNV segments from all chromosomes together) should finish in seconds. It may be a filesystem issue or your data was in a format that the segmentation algorithm did not like and thus failed to produce any segments. Please check our online help on how to check those files.
Hi, I am trying to get results for purity and ploidy using your pipeline. But somehow the tool is stuck for 2 days at this step:
I called it like this:
'./main.py -c configure -t /mnt/Tumor.bam -n /mnt/Normal.bam -o /mnt/accucopy_output/ --nCores 30'
Any suggestions?What would be the fastest way to get just purity/ploidy results, based on either FASTQ, BAM or copynumer files. Thanks!