Job <hint tl -m /data/aryee/bernstein/hic/firecloud/BRD3187.hic -f juicer --refdir /data/aryee/bernstein/hic/structuralVariants/hint_data/hg19_ref --backdir /data/aryee/bernstein/hic/structuralVariants/hint_data/hg19_back/ -g hg19 -n prueba -c 0.05 --ppath /data/aryee/areyes/software/bin/pairix -p 12 -o BRD3187_hint -p 3> was submitted from host <rgs13> by user <ar87> in cluster <cmucluster>.
Job was executed on host(s) <3*cn034>, in queue <big-multi>, as user <ar87> in cluster <cmucluster>.
</PHShome/ar87> was used as the home directory.
</data/aryee/bernstein/hic/structuralVariants> was used as the working directory.
Started at Mon Oct 14 09:55:19 2019
Results reported at Mon Oct 14 13:34:03 2019

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
hint tl -m /data/aryee/bernstein/hic/firecloud/BRD3187.hic -f juicer --refdir /data/aryee/bernstein/hic/structuralVariants/hint_data/hg19_ref --backdir /data/aryee/bernstein/hic/structuralVariants/hint_data/hg19_back/ -g hg19 -n prueba -c 0.05 --ppath /data/aryee/areyes/software/bin/pairix -p 12 -o BRD3187_hint -p 3
------------------------------------------------------------

Exited with exit code 1.

Resource usage summary:

   CPU time   :  35537.62 sec.
   Max Memory :     30148 MB
   Max Swap   :     39641 MB

   Max Processes  :        17
   Max Threads    :        27

The output (if any) follows:

[09:55:20] Argument List: 
[09:55:20] Hi-C contact matrix = /data/aryee/bernstein/hic/firecloud/BRD3187.hic
[09:55:20] Hi-C contact matrix format = juicer
[09:55:20] Genome = hg19
[09:55:20] Name = prueba
[09:55:20] Output directory = BRD3187_hint
[09:55:20] Prepare Matrices!
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[10:02:12] Get matrix Info!
/data/aryee/bernstein/hic/structuralVariants/hint_data/hg19_back/1Mb
/data/aryee/bernstein/hic/structuralVariants/hint_data/hg19_back/100kb
[10:16:53] Rank Product Done: find rank product for each chromosomal pair from BRD3187_hint/prueba_chrompairs_rankProduct.txt. ;)
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[1] "chr1_chr14"[1]
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/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1115: RuntimeWarning: All-NaN slice encountered
 overwrite_input=overwrite_input)
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:304: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1371: RuntimeWarning: All-NaN slice encountered
 overwrite_input=overwrite_input, interpolation=interpolation
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:416: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:377: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:340: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1112: RuntimeWarning: Mean of empty slice
 return np.nanmean(a, axis, out=out, keepdims=keepdims)
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:291: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:328: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:364: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:401: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/numpy/lib/nanfunctions.py:1367: RuntimeWarning: Mean of empty slice
 return np.nanmean(a, axis, out=out, keepdims=keepdims)
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:274: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:314: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:350: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:387: RuntimeWarning: Mean of empty slice
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:189: RuntimeWarning: divide by zero encountered in double_scalars
/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py:190: RuntimeWarning: divide by zero encountered in double_scalars
['39', '128', '137', '715', '1424', '1435', '2485', '1428'] ['954', '1961', '917']
[]
['39', '61', '1424', '1435', '2485', '1428'] ['467', '504', '31']
[]
['1424', '1435', '2485', '1425'] ['40', '85', '94', '496', '0']
[]
merge 0.0 9142.782 4387.095 0.0 4434.713 7243.269 2.0840173280952428 1.6333117836486828
['35', '697', '1424', '1435', '2485', '1428'] ['12', '1310', '1501']
[]
['39', '1424', '1435', '2485'] ['1658', '1701', '3']
[]
['39', '1205', '1424', '1435', '2485', '1428'] ['1426', '1443', '1425']
[]
['39', '61', '128', '299', '1205', '1424', '1435', '2485'] ['922', '1367', '1373', '1384', '1205']
[]
['39', '128', '1424', '1435', '1428'] ['422', '1332', '423']
[]
['39', '1424', '1435', '1428'] ['24', '43', '1347']
[]
['35', '1424', '1435', '2485', '1428'] ['1306']
[]
['39', '61', '300', '1424', '1435', '2485', '1428'] ['1022', '1065', '1072']
[]
['39', '128', '137', '647', '1424', '1435'] ['180', '94']
[]
['39', '61', '128', '137', '1424', '1435', '1724'] ['251', '544']
[]
['39', '59', '137', '465', '1424', '1435', '2485'] ['771', '765']
[]
['39', '1214', '1424', '1435', '1712', '2247'] ['243', '306']
[]
['137', '299', '1424', '1435', '1825', '2344'] ['93', '101', '111', '96']
['39', '128', '494', '635', '1205', '1863', '1976', '387'] ['488', '502', '484']
[]
['39', '61', '1424', '1435', '2485', '1428'] ['26', '1490', '1538', '1544', '1532']
[]
['868', '882', '916', '923', '954', '960'] ['18', '85', '386', '392', '390']
['317', '868', '2309', '2398', '2415', '0'] ['243', '306']
[]
['14', '982', '1307', '2307', '1'] ['93', '101', '111', '428', '99']
['6', '2301', '2341', '2415', '2406'] ['488', '502', '353']
[]
['85', '175', '1282', '542'] ['243', '308']
[]
['5', '17', '85', '94', '496', '832', '1246', '1389', '0'] ['243', '276', '300']
[]
merge 262.603 470.317 206.025 219.753 303.96999999999997 441.14200000000005 2.282815192331028 1.4512682172582825
['85', '94', '496', '874', '881', '1719', '1716'] ['93', '101', '111', '153', '99']
['17', '85', '94', '496', '1156', '1398', '1554', '1835', '495'] ['167', '168']
[]
['458', '495', '559', '574', '570'] ['194', '1122', '199']
['12', '1305', '1493', '1501', '1308'] ['318', '332', '348', '462', '335']
[]
merge 11106.797999999999 13410.794 937.62 741.4010000000001 710.143 8074.544 14.303016147266483 11.370307107160107
['458', '1166', '1310', '1328', '1392', '1400', '1483', '1501', '1308'] ['219', '251', '2']
['458', '495', '1305', '1492', '1501', '1674', '1308'] ['243', '276', '277']
[]
merge 1319.473 1258.68 575.431 398.8879999999999 738.3300000000002 809.2740000000001 2.1873691198423444 1.0960871155174514
['15', '566', '574', '1310', '572'] ['93', '101', '111', '109']
['117', '458', '1305', '1492', '1501', '1673', '1307'] ['167', '356', '354']
[]
['1554', '1701', '1705'] ['222', '251', '252']
[]
['578', '714', '720', '927', '1431', '1661', '715'] ['93', '101', '111', '99']
['64', '373', '417', '477', '1554', '1662', '1701', '1707'] ['356', '470', '488', '495', '502', '499']
[]
['20', '381', '1499', '1544', '1588'] ['215', '251', '492', '252']
[]
['20', '1499', '1590'] ['171', '434', '174']
[]
['665', '664'] ['456', '725', '541']
['433', '1393', '1426', '1438', '1458', '3'] ['243', '281', '429', '438', '309']
[]
['13', '429', '1317', '1426', '890'] ['93', '101', '111', '407', '99']
[]
['190', '217', '433', '752', '1203', '1391', '1443', '1430'] ['167', '356', '435', '172']
[]
['1166', '1222', '1302', '1367', '1373', '1384', '1403', '1407'] ['167', '356', '475', '488', '495', '484']
[]
['422', '1057', '1332', '320'] ['93', '101', '111', '99']
['459', '502', '782', '1204', '1155'] ['93', '101', '111', '336', '407', '99']
[]
['455'] ['157', '268', '317', '335']
['1325', '475'] ['251', '544']
[]
['385', '725', '895', '1018', '1325', '1318'] ['167', '502', '483']
[]
['295', '326', '1142', '325'] ['188', '195', '256', '262', '293', '301', '507']
['1086', '1121', '675'] ['93', '101', '111', '107']
[]
['513', '679', '932', '996', '958'] ['93', '101', '111', '336', '99']
[]
['282', '303', '318', '332', '338'] ['226', '281', '438', '297']
[]
['45', '142', '661', '706', '524'] ['93', '100', '106', '99']
[]
['62'] ['171', '475', '488', '487']
[]
['192', '232', '281', '428', '447', '228'] ['101', '111', '238']
Traceback (most recent call last):
 File "/PHShome/ar87/hint_python_rgs13/bin/hint", line 4, in <module>
   __import__('pkg_resources').run_script('HiNT-Package==2.1.9', 'hint')
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/pkg_resources/__init__.py", line 666, in run_script
   self.require(requires)[0].run_script(script_name, ns)
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1469, in run_script
   exec(script_code, namespace, namespace)
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/EGG-INFO/scripts/hint", line 201, in <module>
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/EGG-INFO/scripts/hint", line 197, in main
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/runhint.py", line 123, in translrun
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py", line 502, in getValidRoughBP
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py", line 233, in filtering
 File "/PHShome/ar87/hint_python_rgs13/lib/python3.6/site-packages/HiNT_Package-2.1.9-py3.6.egg/HiNT/getRoughBreakpoints.py", line 192, in mergeBPs
IndexError: index 1125 is out of bounds for axis 0 with size 592