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Hello,
I been getting different errors when running IDR.
If I run Idr v2.0.2 I get the following error:
./idr --input-file-type bed --rank 7 --plot --verbose --samples peaks_TGATCA_clean.bed peaks_PrNotT_clean.bed
Loading the peak files
Merging peaks
Ranking peaks
Initial parameter values: [0.10 1.00 0.20 0.50]
Fitting the model parameters
Iter 0 1.57e+00 4.57e-01 [0.09023906 0.71172818 0.98999476 0.98043616]
Iter 1 2.36e-01 3.29e-01 [0.1093229 0.49997562 0.98999476 0.9755989 ]
Iter 2 1.56e-01 2.29e-01 [0.1093229 0.34967449 0.98999476 0.97019152]
Iter 3 1.12e-01 1.59e-01 [0.1093229 0.24417437 0.98999476 0.96406317]
Iter 4 4.48e-02 6.87e-02 [0.1093229 0.20000658 0.98999476 0.96466309]
Iter 5 2.89e-03 3.72e-03 [0.1093229 0.20000658 0.98999476 0.9675544 ]
Iter 6 1.44e-03 1.86e-03 [0.1093229 0.20000658 0.98999476 0.96899706]
Iter 7 7.46e-04 9.61e-04 [0.1093229 0.20000658 0.98999476 0.96974351]
Iter 8 3.85e-04 4.96e-04 [0.1093229 0.20000658 0.98999476 0.9701287 ]
Iter 9 2.01e-04 2.58e-04 [0.1093229 0.20000658 0.98999476 0.97032952]
Iter 10 1.06e-04 1.36e-04 [0.1093229 0.20000658 0.98999476 0.97043521]
Iter 11 5.60e-05 7.20e-05 [0.1093229 0.20000658 0.98999476 0.97049116]
Iter 12 2.97e-05 3.82e-05 [0.1093229 0.20000658 0.98999476 0.97052088]
Iter 13 1.58e-05 2.04e-05 [0.1093229 0.20000658 0.98999476 0.9705367 ]
Iter 14 8.42e-06 1.08e-05 [0.1093229 0.20000658 0.98999476 0.97054513]
Iter 15 4.49e-06 5.78e-06 [0.1093229 0.20000658 0.98999476 0.97054962]
Iter 16 2.39e-06 3.08e-06 [0.1093229 0.20000658 0.98999476 0.97055201]
Iter 17 0.00e+00 0.00e+00 [0.1093229 0.20000658 0.98999476 0.97055201]
Finished running IDR on the datasets
Final parameter values: [0.11 0.20 0.99 0.97]
Writing results to file
./idr --input-file-type bed --rank 7 --plot --verbose --samples peaks_TGATCA_clean.bed peaks_PrNotT_clean.bed
Traceback (most recent call last):
File "./idr", line 10, in
idr.idr.main()
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.2-py3.7-linux-x86_64.egg/idr/idr.py", line 774, in main
useBackwardsCompatibleOutput=args.use_old_output_format)
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.2-py3.7-linux-x86_64.egg/idr/idr.py", line 415, in write_results_to_file
if localIDRs == None or IDRs == None:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
If I run Idr v2.0.3 I get:
./idr --input-file-type bed --rank 7 --plot --verbose --samples ENCFF437QMO.bed ENCFF025CWO.bed
Traceback (most recent call last):
File "./idr", line 10, in
idr.idr.main()
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 828, in main
merged_peaks, signal_type = load_samples(args)
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 726, in load_samples
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 726, in
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 64, in load_bed
float(data[6]), float(data[7]), float(data[8])
ValueError: could not convert string to float: 'chr1_minus_88541_827795'
My bed files were generated using grit (following scrip from encode rampage protocol) and are organized as follow:
Hello,
I been getting different errors when running IDR.
If I run Idr v2.0.2 I get the following error:
./idr --input-file-type bed --rank 7 --plot --verbose --samples peaks_TGATCA_clean.bed peaks_PrNotT_clean.bed
Loading the peak files
Merging peaks
Ranking peaks
Initial parameter values: [0.10 1.00 0.20 0.50]
Fitting the model parameters
Iter 0 1.57e+00 4.57e-01 [0.09023906 0.71172818 0.98999476 0.98043616]
Iter 1 2.36e-01 3.29e-01 [0.1093229 0.49997562 0.98999476 0.9755989 ]
Iter 2 1.56e-01 2.29e-01 [0.1093229 0.34967449 0.98999476 0.97019152]
Iter 3 1.12e-01 1.59e-01 [0.1093229 0.24417437 0.98999476 0.96406317]
Iter 4 4.48e-02 6.87e-02 [0.1093229 0.20000658 0.98999476 0.96466309]
Iter 5 2.89e-03 3.72e-03 [0.1093229 0.20000658 0.98999476 0.9675544 ]
Iter 6 1.44e-03 1.86e-03 [0.1093229 0.20000658 0.98999476 0.96899706]
Iter 7 7.46e-04 9.61e-04 [0.1093229 0.20000658 0.98999476 0.96974351]
Iter 8 3.85e-04 4.96e-04 [0.1093229 0.20000658 0.98999476 0.9701287 ]
Iter 9 2.01e-04 2.58e-04 [0.1093229 0.20000658 0.98999476 0.97032952]
Iter 10 1.06e-04 1.36e-04 [0.1093229 0.20000658 0.98999476 0.97043521]
Iter 11 5.60e-05 7.20e-05 [0.1093229 0.20000658 0.98999476 0.97049116]
Iter 12 2.97e-05 3.82e-05 [0.1093229 0.20000658 0.98999476 0.97052088]
Iter 13 1.58e-05 2.04e-05 [0.1093229 0.20000658 0.98999476 0.9705367 ]
Iter 14 8.42e-06 1.08e-05 [0.1093229 0.20000658 0.98999476 0.97054513]
Iter 15 4.49e-06 5.78e-06 [0.1093229 0.20000658 0.98999476 0.97054962]
Iter 16 2.39e-06 3.08e-06 [0.1093229 0.20000658 0.98999476 0.97055201]
Iter 17 0.00e+00 0.00e+00 [0.1093229 0.20000658 0.98999476 0.97055201]
Finished running IDR on the datasets
Final parameter values: [0.11 0.20 0.99 0.97]
Writing results to file
./idr --input-file-type bed --rank 7 --plot --verbose --samples peaks_TGATCA_clean.bed peaks_PrNotT_clean.bed
Traceback (most recent call last):
File "./idr", line 10, in
idr.idr.main()
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.2-py3.7-linux-x86_64.egg/idr/idr.py", line 774, in main
useBackwardsCompatibleOutput=args.use_old_output_format)
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.2-py3.7-linux-x86_64.egg/idr/idr.py", line 415, in write_results_to_file
if localIDRs == None or IDRs == None:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
If I run Idr v2.0.3 I get:
./idr --input-file-type bed --rank 7 --plot --verbose --samples ENCFF437QMO.bed ENCFF025CWO.bed
Traceback (most recent call last):
File "./idr", line 10, in
idr.idr.main()
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 828, in main
merged_peaks, signal_type = load_samples(args)
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 726, in load_samples
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 726, in
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/rhome/icoimbra/.conda/envs/py3_env/lib/python3.7/site-packages/idr-2.0.3-py3.7-linux-x86_64.egg/idr/idr.py", line 64, in load_bed
float(data[6]), float(data[7]), float(data[8])
ValueError: could not convert string to float: 'chr1_minus_88541_827795'
My bed files were generated using grit (following scrip from encode rampage protocol) and are organized as follow:
chr1 629361 629492 TSS_chr1_minus_13397_827795_pk1 1000 - 15.0 chr1_minus_13397_827795 chr1_minus_13397_827795 TSS_chr1_minus_13397_827795_pk1 1.0,0.0,0.0,0.0,0.0,0.0,1.0,2.0,0.0,0.0,0.0,0.0,0.0,0.0$
chr1 629580 629610 TSS_chr1_minus_13397_827795_pk2 1000 - 17.0 chr1_minus_13397_827795 chr1_minus_13397_827795 TSS_chr1_minus_13397_827795_pk2 2.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0$
chr1 629639 629939 TSS_chr1_plus_629080_634923_pk1 1000 + 1646.0 chr1_plus_629080_634923 chr1_plus_629080_634923 TSS_chr1_plus_629080_634923_pk1 270.0,0.0,0.0,1.0,79.0,6.0,4.0,2.0,3.0,23.0,8.0,97.0,0.$
chr1 629752 629867 TSS_chr1_minus_13397_827795_pk3 1000 - 37.0 chr1_minus_13397_827795 chr1_minus_13397_827795 TSS_chr1_minus_13397_827795_pk3 2.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.0,0.0,1.0$
chr1 629968 630009 TSS_chr1_minus_13397_827795_pk4 1000 - 97.0 chr1_minus_13397_827795 chr1_minus_13397_827795 TSS_chr1_minus_13397_827795_pk4 41.0,0.0,0.0,0.0,3.0,0.0,0.0,0.0,0.0,3.0,0.0,0.0,0.0$
I am using Python 3.7.6
How do I work around this?
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