Excuse me, I give an example with CCS input, but I get 'no pa file' and no output information.
python RepeatHMM/bin/repeatHMM.py Scan --SeqTech "Pacbio"
--Patternfile ../chr1_filter_FP.list --envset repeathmmenv
--Onebamfile ../bam_chr1_8000000_100000000.bam
--hgfile ../chr1.fa --hg hg38
--thread 50 --UserDefinedUniqID chr1scan --SplitAndReAlign 2 --outFolder output --repeatName all
question:
('No pa file ', '../envs/repeathmmenv/lib/python2.7/site-packages/RepeatHMM/reference_sts//hg38/hg38.predefined.pa')
Please tell me how to solve it. Waiting for your answer~
Excuse me, I give an example with CCS input, but I get 'no pa file' and no output information.
python RepeatHMM/bin/repeatHMM.py Scan --SeqTech "Pacbio"
--Patternfile ../chr1_filter_FP.list --envset repeathmmenv
--Onebamfile ../bam_chr1_8000000_100000000.bam
--hgfile ../chr1.fa --hg hg38
--thread 50 --UserDefinedUniqID chr1scan --SplitAndReAlign 2 --outFolder output --repeatName all
question:
('No pa file ', '../envs/repeathmmenv/lib/python2.7/site-packages/RepeatHMM/reference_sts//hg38/hg38.predefined.pa')
Please tell me how to solve it. Waiting for your answer~