qbrc / pipe-clip Goto Github PK

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,

Hi!!

The galaxy site is down again!!

Many thanks for your help

We are attempting to get PIPE-SEQ working on the SHARCNET, but we are having trouble installing the Python dependency "ghmm" due to its age. It is also not available on the PIP python package system. Are you aware of any alternatives that may work with PIPE-SEQ for this particular function?

Thank you.

Hey,

We have been using your pipeline for data analysis and I noticed that the QBRC-Galaxy site is down with the following error message (Forbidden
You don't have permission to access / on this server.
Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.)

Please help and many thanks!

hello！i have a problem when i use pipe-clip. my data is in fly cells, but the parameter -s has only two options (mm & hg).
how could i make it for drosophila data ?
thank you very much for help !!!

(base) Xiaos-MacBook-Pro-3:PIPE-CLIP-1.2.0-alpha xiaolei$ python pipeclip.py -i /miniconda3/data/hnRNP_U/aln-hnRNPU.sorted.bam -o test
Traceback (most recent call last):
File "pipeclip.py", line 13, in
from lib import *
File "/miniconda3/bin/PIPE-CLIP-1.2.0-alpha/lib/init.py", line 2, in
import Alignment
ModuleNotFoundError: No module named 'Alignment'

Hi!

I was wondering, It's been a week or so since the Galaxy Site can’t be reached, is this going to be permanent? We've used your pipeline for some of your analysis and we will be publishing soon. But we can't access and update the results!

Thank you very much,

I have finally installed all dependencies (including python packages pybedtools and ghmm), and I get the following error when attempting to run the program:

python pipeclip.py -i ERR_TopHat_Aligned.bam -o ERR-NoRepeatRemoval -c 3 -l 25 -m 2 -r 0 -M 0.05 -C 0.05 -s hg19

Traceback (most recent call last):
File "pipeclip.py", line 13, in
from lib import *
File "/project/xxxxx/emucaki/RNPS1-FASTQ/PIPE-CLIP-master/lib/init.py", line 2, in
import Alignment
File "/project/xxxxx/emucaki/RNPS1-FASTQ/PIPE-CLIP-master/lib/Alignment.py", line 6, in
import Enrich
File "/project/xxxxx/emucaki/RNPS1-FASTQ/PIPE-CLIP-master/lib/Enrich.py", line 15, in
from pysam import *
AttributeError: 'module' object has no attribute 'TupleProxy'

Any help would be most appreciated.

on mac os x mavericks, the inputProcess.py file does not accurately detect the header for the bam file.