runtime error about methyldackel HOT 4 CLOSED

That's a new one, can you post the command you're using?

from methyldackel.

Hi,
I have aligned the data with last, marked duplicates with picard and converted to legacy-cigar with rtg sammerge. I used as reference human_g1k_v37_decoy.fasta

The call to PileOmeth is
ref=human_g1k_v37_decoy.fasta.gz
./PileOMeth/PileOMeth extract -r 21 -o pile/F1F $ref F1F.chr_21.bam

I have tested with a subset of just 50k reads selecting a sug-region in chr21. I got the same error message, the difference was that I got some more data in bedGraph file. Before was empty (only header), now has:

track type="bedGraph" description="minisample CpG methylation levels"
21 9500005 9500006 0 0 2
21 9500026 9500027 33 1 2
21 9500064 9500065 100 3 0
21 9500253 9500254 0 0 1

from methyldackel.

Could you make the BAM file available to me? If it's just 50K reads you can likely just email it to my ([email protected]).

from methyldackel.

Can you try the 0.1.12 release? I fixed handling of hard-clipped bases in that, which was the cause of this issue. Hopefully that will get things working on your full files.

from methyldackel.