daler / chromhmm-tools Goto Github PK

Hello,

I am receiving an error when using the ChromHMM-signalize rebin command. The first bigwig file is converted to a bedgraph and then I receive the error below. Do you have any suggestions to resolve this?

Thanks,
Michael

[2018-02-24 23:52:41,283] INFO: /projects/med/hlab/analysis/working/UM_shBAP1/ChIP-Seq/921/chromHMM/921_Control_H2Aub_average.bw -> binned/921_Control-H2Aub-200-{chrom}.binned
[2018-02-24 23:52:41,353] INFO: converting to bedgraph
[2018-02-24 23:53:46,457] INFO: chr1
Traceback (most recent call last):
 File "/projects/med/hlab/software/chromhmm-tools/chromhmm_signalize.py", line 280, in <module>
 parser.dispatch()
 File "/projects/med/hlab/software/virtualpython/ENV/lib/python2.7/site-packages/argh/helpers.py", line 55, in dispatch
 return dispatch(self, *args, **kwargs)
 File "/projects/med/hlab/software/virtualpython/ENV/lib/python2.7/site-packages/argh/dispatching.py", line 174, in dispatch
 for line in lines:
  File "/projects/med/hlab/software/virtualpython/ENV/lib/python2.7/site-packages/argh/dispatching.py", line 277, in _execute_command
 for line in result:
File "/projects/med/hlab/software/virtualpython/ENV/lib/python2.7/site-packages/argh/dispatching.py", line 260, in _call
    result = function(*positional, **keywords)
  File "/projects/med/hlab/software/chromhmm-tools/chromhmm_signalize.py", line 194, in rebin
    write_interpolated_results(x, y, chrom)
  File "/projects/med/hlab/software/chromhmm-tools/chromhmm_signalize.py", line 176, in write_interpolated_results
    max_pos = genome[chrom][-1]
KeyError: u'chr1'

Hi, I'm trying to run rebin on a set of .bigwig files, however this error shows up when I try to run chromhmm_signalize.py rebin config.txt hg18. The config.txt file looks correct, so I'm not sure what the error is. I tried to use a config file with only one line, or config files with other .bigwig files from ENCODE, but both still show the same error. Please help! Thank you :)

Code
chromhmm_signalize.py rebin config.txt hg18

CONFIG.TXT

ERROR
INFO: /home/itg/jackson.cheung/data/GSM3691940_MSC_H3K4me3_8A.bigwig -> binned/MSC-H3K4me3-200-{chrom}.binned
Traceback (most recent call last):
File "/home/itg/jackson.cheung/chromhmm-tools/chromhmm_signalize.py", line 280, in
parser.dispatch()
File "/home/itg/jackson.cheung/miniconda3/envs/HiCExplorer/lib/python3.10/site-packages/argh/helpers.py", line 55, in dispatch
return dispatch(self, *args, **kwargs)
File "/home/itg/jackson.cheung/miniconda3/envs/HiCExplorer/lib/python3.10/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/home/itg/jackson.cheung/miniconda3/envs/HiCExplorer/lib/python3.10/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/home/itg/jackson.cheung/miniconda3/envs/HiCExplorer/lib/python3.10/site-packages/argh/dispatching.py", line 260, in _call
result = function(*positional, **keywords)
File "/home/itg/jackson.cheung/chromhmm-tools/chromhmm_signalize.py", line 192, in rebin
for i in bt:
File "pybedtools/cbedtools.pyx", line 760, in pybedtools.cbedtools.IntervalIterator.next
File "/home/itg/jackson.cheung/miniconda3/envs/HiCExplorer/lib/python3.10/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfc in position 1: invalid start byte

I checked the results generated by chromhmm_signalize.py which all results are float values. It is correct?

Hi,

I hope this repo is still maintained, it looks a very useful tool from my first tries, thanks for your work.

I am currently having trouble pooling multiple instances of the binarized signal into a single one when going from your script to ChromHMM.

For instance, I have 15 H3K27ac peak files, same cell type. However, even specifying this in the config, I obtain a single column for each one of them in the signal folder. Am I missing something?

It looks like ChromHMM binarizeSignal doesn't allow for a config file specification itself (unlike binarizeBed and binarizeBam), so I can't pool them downstream.

Thank you for your help

EDIT: I made a mistake, indeed the output of your script is a single file for each cell/mark combination, for each chromosome (pooling the bw/bedgraphs, right? But, looking at the logs while the program is running it almost seems that each single one overwrites the previous). The problem is probably downstream when I first call ChromHMM. I am trying to understand what step is causing me this problem.