HeejunJang

I installed manta succesfully but there's an issue running demo **** Starting demo configuration and run. **** Configuration cmd: "/work/tools/manta/bin/configManta.py" --normalBam="/work/tools/manta/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam" --tumorBam="/work/tools/manta/share/demo/manta/data/G15512.HCC1954.1.COST16011_region.bam" --referenceFasta="/work/tools/manta/share/demo/manta/data/Homo_sapiens_assembly19.COST16011_region.fa" --region=8:107652000-107655000 --region=11:94974000-94989000 --exome --runDir="MantaDemoAnalysis" Traceback (most recent...

Runtime error while running batch process

6

Hello, I ran cnvkit on conda environment. Here's my command cnvkit.py batch $INPUT/$i".recal.bam" -n \ --targets $REF/bed/snuh_nicu_sort.bed \ --fasta $REF/hg19/hg19_1-22-X-Y-M.fa \ --access $CNVKIT/data/access-5k-mappable.hg19.bed \ --output-reference $FINAL/$i".cnn" \ --output-dir $FINAL Here's...

Examining conflicts takes forever installing cnvkit with conda

3

Hello I tried to install cnvkit using conda. However, it is currently unfinished on the 3rd day. Only the process of "Examing conflicts ~~" is being repeated over and over...

Rscript runtime Error occurred

5

Hello I'll report another issues. Segmenting /work/hjjang/CNV/result/20221005/F20220718_js-yoon_001_41.markdup/F20220718_js-yoon_001_41.markdup.cnr ... Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes Traceback (most recent call last): File "/work/tools/cnvkit/cnvkit.py", line 9, in args.func(args) File...