Comments (2)
Hi, Yanxiao et al.
Did you every come across a solution for this problem? I am experiencing the same thing when running idr.py either as a standalone module or through the ENCODE ATAC-Seq pipeline (atac.bds):
Traceback (most recent call last):
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/bin/idr", line 4, in <module>
__import__('pkg_resources').run_script('idr==2.0.3', 'idr')
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/pkg_resources/__init__.py", line 748, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/pkg_resources/__init__.py", line 1517, in run_script
exec(code, namespace, namespace)
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in <module>
idr.idr.main()
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 840, in main
merged_peaks, signal_type = load_samples(args)
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 760, in load_samples
oracle_pks, args.use_nonoverlapping_peaks)
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 281, in merge_peaks
use_nonoverlapping_peaks=use_nonoverlapping_peaks)
File "/gpfs/gpfs1/home/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 223, in merge_peaks_in_contig
all_intervals.sort()
TypeError: unorderable types: int() < NoneType()
I tried printing out the all_intervals[] array and can find instances of lines that look like this:
(Peak(chrm='chr1', strand='.', start=176983596, stop=176983716, signal=2.66479, summit=None, signalValue=2.65491, pValue=2.66479, qValue=0.72361), 0),
I too have found that there are "-1" summit values called by MACS2 that are being converted to "None" when run through idr.py, which apparently is causing the all_intervals.sort() function to not work, (presumably its sorting based on windows around summit values?)
I suppose this may be a MACS2 callpeak error and not idr related, per se, but was wondering if you had a work around or identified a cause of these -1 summit values.
Considering just removing these peak rows as "Fails" before running Idr....
from idr.
@hardigan Sorry I don't...I did not get any response here and just gave up on it. I guess if you remove or convert the -1 summit values, it will bypass that problem, but I don't know how this might change the outcome.
from idr.
Related Issues (20)
- Empty merged picks list HOT 2
- Order of Peak1 vs. Peak2 after --samples HOT 1
- ValueError: could not convert string to float
- bug found? HOT 1
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- Can I use IDR to analyze ChIPseq or Cuttag data of histones?
- IDR with small number of peaks
- Error running with bed file
- ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() HOT 5
- idr excludes top peaks HOT 1
- idr --samples peak1 peak2 : Number of peaks passing IDR cutoff of 0.05 - 0/50537 (0.0%) HOT 1
- error: Use a.any() or a.all()_ HOT 3
- pkg_resources.DistributionNotFound
- Parameter requirements for input file in BED format?
- installation issues
- IDR-pooled peak list
- idr:idr has no attribute 'fit_model_and_calc_local_idr'
- Irreproducible Discovery Rate (IDR) for 3 replicates HOT 3
- AttributeError: module 'numpy' has no attribute 'int' HOT 2
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from idr.