Yu S. Huang

Instructions on how to run are now included in https://github.com/polyactis/Accucopy/README.md.

Please check https://www.yfish.org/display/PUB/Accucopy#Accucopy-cnv.output.tsv cp is the total copy number. major_allele_cp is the copy number for the major allele (=major_cn of Pyclone VI?). We are not familiar with PYClone VI... --...

This looks quite strange. pyflow is the software that connects all components together. Do you know which step it was running when this error occurred? If you re-run the same...

@WuRAFY the error was due to 1) a bug in handling UID inside a container (fixed and updated in the dockerhub image); 2) the bam header contains contig IDs that...

Can you show more log messages before the screenshot? The screenshot is the plotting program complaining about the missing input file (model selection result). But this is usually due to...

The purity/ploidy/CNA inference part failed (log below), but without apparent reason. Can you send me /data/test_out1/all_segments.tsv.gz, /data/test_out1/het_snp.tsv.gz , /data/refData/genome.dict? ... Inferring the best period by log likelihood from 2 candidates...

Apologies for the late reply! Was only able to check this email a few days ago :) There was a stupid bug in our program that puts a limit on...

Interesting to hear that someone is trying Accucopy on a dog tumor! Finally! That's why we spent effort to make it possible for users to make their own reference genomes....

Did you check if chr33 is in your genome index files (i.e. genome.dict and etc.)?

Then it probably failed in these filters. You can check https://samtools.github.io/hts-specs/SAMv1.pdf on how to know if a read is properly paired, if its mate is unmapped, what the insert size...