Closed biozzq closed 3 years ago
Hi There,
I just re-tested the latest release on local data and it worked fine. I don't think any updates from the past two months (just a few small bug fixes) would cause this.
One thing might be the goldenPath data. In an earlier comment from January, your specified command was at 100kb resolution; this one is at 50kb. Since the goldenPath is binned at the resolution of download, you will need a new folder for this run.
Dear @ay-lab
Yes, you are right, this error is caused by the different resolution. However, I wonder that how to prepare the goldenPath GC/TSS data at specific resolution? Thank you.
Best wishes, Zheng zhuqing
Thank you for raising this concern—this is an important thing to note. If you don't specify "-alignData" in the arguments, dcHiC will re-download the goldenPath data at the given resolution. I would run one chromosome standalone at the new resolution, have dcHiC download the data, and then run the rest using that directory.
Dear all,
When running following command, the program will exit with the error,
No such file or directory: 'hmfa_chrRAW_10MF-1_exp_1.txt'
. However, I remember I can run without any errors about two months ago, after updating the version of dcHiC, now the program fails.python dchic/dchic.py -res 50000 -inputFile ${pre}.txt -parallel 6 -chrFile chr.txt -input 2 -genome mm10 -alignData goldenpathData -keepIntermediates 1 -blacklist mm10-blacklist.v2.bed
Sincerely, Zheng zhuqing