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View Code? Open in Web Editor NEWDNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
Home Page: https://pmbio.github.io/pycoMeth/
License: GNU General Public License v3.0
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
Home Page: https://pmbio.github.io/pycoMeth/
License: GNU General Public License v3.0
Hi,
I am trying to install pycometh in a Docker image but I can't get it to install. As a minimal example, try this dockerfile
`
FROM condaforge/mambaforge
RUN mamba install -c aleg -c plotly -c bioconda -c anaconda pycometh
`
This gives the following error:
[2/2] RUN mamba install -c aleg -c plotly -c bioconda -c anaconda pycometh:
#6 7.760
#6 7.760 Looking for: ['pycometh']
#6 7.760
#6 7.760
#6 7.760 Pinned packages:
#6 7.760 - python 3.10.*
#6 7.760
#6 7.760
#6 7.760 Encountered problems while solving:
#6 7.760 - nothing provides openssl >=1.0.2p,<1.0.3a needed by python-3.6.7-hd21baee_1002
openssl is part of anaconda channel, so not sure why this can't be installed.
Any advice appreciated!
Hi, an error was appeared when I run 'pycoMeth Comp_Report':
'Cannot import dependencies required for static image export'. I noticed that this error occurred when I installed the software and ran the ‘pycoMeth -h’ command.
Can you help me? Thank you !
Hello,
Because of the improvements in modified basecalling accuracy Nanopolish
states that it does not support R10 flowcells on its GitHub. It also seems that Oxford Nanopore is investing in this new tool suite called Modkit for analysis of base modification. I was wondering if there are any plans for pycoMeth to start supporting the bedMethyl
files created by the pileup
function from modkit
? Alternatively, do you know of a way to convert the bedMethyl
files from modkit
into the MetH5
format from Nanopolish
so that they are compatible with pycoMeth
?
I really like the ease of use and great features included in pycoMeth. It would be great to be able to easily integrate it with the new R10 data pre-processed using modkit
.
Hi @here I am trying to install this package using pip and conda but I have been having a series of errors, is there a possibility of getting any other ways to install it?
Dear Rene,
I cannot access the pycoMeth documentation.
Best,
Madalina
Dear pycoMeth developer(s),
I am trying using pycometh Meth_Comp to do methylation differential analysis. My command was pycometh Meth_Comp -i 1.m5 2.m5 3.m5 4.m5 5.m5 -f reference.fa -b output.bed
.
It reported error as the following:
Cannot import dependencies required for static image export
## Checking options and input files ##
## Opening H5 files ##
Starting asynchronous file parsing
Launching 4 worker processes
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
No valid p-Value could be computed
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Results summary
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/Meth_Comp.py", line 289, in __call__
label_list, raw_llr_list, raw_pos_list, raw_read_list = self.loader.read_raw_llrs(interval)
File "/home/zhany0s/miniconda3/lib/python3.8/site-packages/pycoMeth/loader.py", line 52, in read_raw_llrs
interval_container = chrom_container.get_values_in_range(interval.start, interval.end)
AttributeError: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
CRITICAL: Error in worker thread
CRITICAL: 'NoneType' object has no attribute 'get_values_in_range'
Exception ignored in: <function Pool.__del__ at 0x2b1a490240d0>
Traceback (most recent call last):
File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/pool.py", line 268, in __del__
self._change_notifier.put(None)
File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/queues.py", line 368, in put
self._writer.send_bytes(obj)
File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/connection.py", line 200, in send_bytes
self._send_bytes(m[offset:offset + size])
File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/connection.py", line 411, in _send_bytes
self._send(header + buf)
File "/home/zhany0s/miniconda3/lib/python3.8/multiprocessing/connection.py", line 368, in _send
n = write(self._handle, buf)
OSError: [Errno 9] Bad file descriptor
I thought it was because of no valid p-values can be used, so I adjusted --pvalue_threshold
but it seemed not help. Would you please let me know what should I do to get it work?
Thank you very much in advance.
Yingzi
Hi,
I'm running command "pycometh Meth_Seg" and encountering an error:
OSError: Unable to open file (unable to open file: name = '[/NAS/wg_hl/pancancer/OSCC/Methylation/f5c_meth/pycoMeth/MetH5/OSCC1/OSCC1_methylate.m5,', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0).
But my file is existing. I don't know how to solve this issue, can you help me?
Hi,
I am interested in using Meth_Comp
for DMR analysis and I already have per-site methylation calling results for 2 samples, they are in BED format with chromosome, start position, end position, and methylation frequency for each site.
Is it possible to use BED file instead of MetH5 in this case? Any hints for the implementation? Thanks.
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