Error: wrong end marker in ./k25/NRDB.unq.kmc_pre
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Hi,
I would like to use CASK and I have started with the database creation. Apart from problems with RepeatMasker input that I was able to solve myself (the script is not suitable for minor changes and there is no specification which column should contain what, apparently the BED output I have downloaded for chm13 2.0 with RepeatMasker was not compatible), I then faced problems at the 92th line of the code:
kmc_tools simple ./k25/NRDB.unq ./k25/by_type/reptype_BKG kmers_subtract ./k25.minusBKG/NRDB.unq**
the output of the previous command
kmc -k25 -m200 -sm -t24 -fm -ci1 -cx1 ../fa/repeats.fa ./k25/NRDB.unq tmp/
seemed to work fine, here is the output:
Stats:
No. of k-mers below min. threshold : 0
No. of k-mers above max. threshold : 1520572631
No. of unique k-mers : 2093088263
No. of unique counted k-mers : 572515632
Total no. of k-mers : 6820729833
Total no. of sequences : 4636653
Total no. of super-k-mers : 762616974
I will be grateful for help, how to proceed. I have spent a lot of time on this database generation already...
Hello Alice, do you have a working CASK pipeline? I would like to start using it but this repository doesn't have much documentation or comments in the code. Please let me know if you have something up and running on chm13 v2.0, that would be amazing!