Can't run PIPECLIP- ERROR: Input file does not have header, later it says OK!!! #5
Description
HI!
I am trying to run PIPECLIP locally, but I am unable to do so. If I begin with a .sam, samtools returns an error. If I use a .bam.bai file, then I get
`:$ python pipeclip.py -i /path/to/Clip.bam.bai -o Clip-Rt14 -c 3 -l 15 -m 5 -r 0 -M 0.05 -C 0.05 -s hg19
INFO:Start to run
[E::hts_open_format] Failed to open file /path/to/Clip.bam.bai
[E::hts_open_format] Failed to open file /path/to/Clip.bam.bai
ERROR:Input file does not have header, please check your file. Program quit
INFO:Input file OK,start to run PIPE-CLIP
INFO:Species info hg19
ERROR:Cannot open input file
INFO:Started to annotate cross-linking sits using HOMER
Traceback (most recent call last):
File "pipeclip.py", line 130, in
runPipeClip(infile,control,outputPrefix,matchLength,mismatch,rmcode,fdrEnrichedCluster,clipType,fdrReliableMutation,species)
File "pipeclip.py", line 97, in runPipeClip
for name in outfilelist:
UnboundLocalError: local variable 'outfilelist' referenced before assignment
`
Would you mind pointing me on which is the problem?
Many thanks,