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nboley / idr

IDR
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IndexError: list index out of range #41

Open aparnasing opened 5 years ago

aparnasing commented 5 years ago

Hi, I am using idr to process 2 replicate bed files but getting an index error. copying command and bash response idr --samples dyadvscolrep1_c3.0_common.bed dyadvscolrep2_c3.0_common.bed /usr/local/bin/idr --samples dyadvscolrep1_c3.0_common.bed dyadvscolrep2_c3.0_common.bed Traceback (most recent call last): File "/usr/local/bin/idr", line 4, in import('pkg_resources').run_script('idr==2.0.3', 'idr') File "/usr/local/lib/python3.6/site-packages/pkg_resources/init.py", line 743, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/local/lib/python3.6/site-packages/pkg_resources/init.py", line 1498, in run_script exec(code, namespace, namespace) File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in idr.idr.main() File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 839, in main merged_peaks, signal_type = load_samples(args) File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 703, in load_samples for fp in args.samples] File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 703, in for fp in args.samples] File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 53, in load_bed signal = float(data[signal_index]) IndexError: list index out of range

melnuesch commented 5 years ago

I got a similar error. Any thoughts?

Traceback (most recent call last): File "/Users/nueschm/miniconda3/bin/idr", line 4, in import('pkg_resources').run_script('idr==2.0.2', 'idr') File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1453, in run_script exec(code, namespace, namespace) File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/EGG-INFO/scripts/idr", line 10, in idr.idr.main() File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 733, in main merged_peaks, signal_type = load_samples(args) File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 620, in load_samples for fp in args.samples] File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 620, in for fp in args.samples] File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 39, in load_bed if peak_summit_index == None or int(data[peak_summit_index]) == -1: IndexError: list index out of range

hjames1 commented 4 years ago

I got a similar error,too.

Traceback (most recent call last): File "/home/u100395/workdir/miniconda3/envs/chipseq/bin/idr", line 10, in idr.idr.main() File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 840, in main merged_peaks, signal_type = load_samples(args) File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 732, in load_samples f1, f2 = [load_bed(fp, signal_index) for fp in args.samples] File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 732, in f1, f2 = [load_bed(fp, signal_index) for fp in args.samples] File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 65, in load_bed float(data[6]), float(data[7]), float(data[8]) IndexError: list index out of range

yx-xu commented 4 years ago

Hello! I got an error same to this, but I couldn't resolve it. Have you solved the problem? Could you help me about this? Thank you very much! Looking forward to your reply!

karl1926 commented 3 years ago

I had a similar issue. Any news?

Suger0917 commented 2 years ago

I had a similar error. File "/storage/xx/software/miniconda3/lib/python3.9/site-packages/idr-2.0.2-py3.9-linux-x86_64.egg/idr/idr.py", line 45, in load_bed peak = Peak(data[0], data[5], IndexError: list index out of range File "/storage/xx/software/miniconda3/lib/python3.9/site-packages/idr-2.0.2-py3.9-linux-x86_64.egg/idr/idr.py", line 45, in load_bed peak = Peak(data[0], data[5], IndexError: list index out of range

Peak score is in the column 5th. In python, actual index is equal to py_index+1. So I set peak = Peak(data[0], data[4] in line 45 of idr.py. This error disappeared.

brottodb commented 1 year ago

I am having a similar problem. Anyone was able to solve this issue? Thanks!

luorongxin-yuan commented 5 months ago

had similar problem at line 65 when my input bed file is 8 columns, but 9 is expected. So I just kept the original 6 columns, and filled column 7-9 with 0s. Seemed to solve the problem, hopefully not interfering with statistics File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 65, in load_bed float(data[6]), float(data[7]), float(data[8]) IndexError: list index out of range