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  1. python3 src/predict.py \
  2. > --enhancers DIPG/ABC_output/Neighborhoods/EnhancerList.txt \
  3. > --genes DIPG/ABC_output/Neighborhoods/GeneList.txt \
  4. > --HiCdir DIPG/input_data/HiC/raw/ \
  5. > --hic_resolution 5000 \
  6. > --scale_hic_using_powerlaw \
  7. > --threshold .02 \
  8. > --cellType E3371K27M \
  9. > --outdir DIPG/ABC_output/Predictions/ \
  10. > --make_all_putative
  11. reading genes
  12. reading enhancers
  13. Making predictions for chromosome: chr17
  14. Making putative predictions table...
  15. Using: DIPG/input_data/HiC/raw/chr17/chr17.KRobserved.gz
  16. Begin HiC
  17. Loading HiC
  18. hic.to.sparse: Elapsed time: 1.595400333404541
  19. HiC Matrix has row sums of 1862.8366265197753, making doubly stochastic...
  20. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  21.   norms[norms < kr_cutoff] = np.nan
  22. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  23.   norms[norms >= kr_cutoff] = 1
  24. HiC has 3242775 rows after windowing between 0 and 5000000
  25. process.hic: Elapsed time: 2.126204252243042
  26. HiC added to predictions table. Elapsed time: 2.452784299850464
  27. HiC Complete
  28. Completed chromosome: chr17. Elapsed time: 10.526445388793945
  29.  
  30. Making predictions for chromosome: chr7
  31. Making putative predictions table...
  32. Using: DIPG/input_data/HiC/raw/chr7/chr7.KRobserved.gz
  33. Begin HiC
  34. Loading HiC
  35. hic.to.sparse: Elapsed time: 4.790992259979248
  36. HiC Matrix has row sums of 1995.5095329172382, making doubly stochastic...
  37. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  38.   norms[norms < kr_cutoff] = np.nan
  39. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  40.   norms[norms >= kr_cutoff] = 1
  41. HiC has 7391896 rows after windowing between 0 and 5000000
  42. process.hic: Elapsed time: 5.008707761764526
  43. HiC added to predictions table. Elapsed time: 2.7514290809631348
  44. HiC Complete
  45. Completed chromosome: chr7. Elapsed time: 16.02497410774231
  46.  
  47. Making predictions for chromosome: chr22
  48. Making putative predictions table...
  49. Using: DIPG/input_data/HiC/raw/chr22/chr22.KRobserved.gz
  50. Begin HiC
  51. Loading HiC
  52. hic.to.sparse: Elapsed time: 0.6104254722595215
  53. HiC Matrix has row sums of 2462.539801718806, making doubly stochastic...
  54. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  55.   norms[norms < kr_cutoff] = np.nan
  56. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  57.   norms[norms >= kr_cutoff] = 1
  58. HiC has 1479373 rows after windowing between 0 and 5000000
  59. process.hic: Elapsed time: 0.8214213848114014
  60. HiC added to predictions table. Elapsed time: 0.9709851741790771
  61. HiC Complete
  62. Completed chromosome: chr22. Elapsed time: 4.107322931289673
  63.  
  64. Making predictions for chromosome: chr18
  65. Making putative predictions table...
  66. Using: DIPG/input_data/HiC/raw/chr18/chr18.KRobserved.gz
  67. Begin HiC
  68. Loading HiC
  69. hic.to.sparse: Elapsed time: 1.4836575984954834
  70. HiC Matrix has row sums of 1336.4652503016298, making doubly stochastic...
  71. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  72.   norms[norms < kr_cutoff] = np.nan
  73. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  74.   norms[norms >= kr_cutoff] = 1
  75. HiC has 3001337 rows after windowing between 0 and 5000000
  76. process.hic: Elapsed time: 2.0175423622131348
  77. HiC added to predictions table. Elapsed time: 0.9745612144470215
  78. HiC Complete
  79. Completed chromosome: chr18. Elapsed time: 5.525629758834839
  80.  
  81. Making predictions for chromosome: chr15
  82. Making putative predictions table...
  83. Using: DIPG/input_data/HiC/raw/chr15/chr15.KRobserved.gz
  84. Begin HiC
  85. Loading HiC
  86. hic.to.sparse: Elapsed time: 1.9200904369354248
  87. HiC Matrix has row sums of 1826.2255878774924, making doubly stochastic...
  88. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  89.   norms[norms < kr_cutoff] = np.nan
  90. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  91.   norms[norms >= kr_cutoff] = 1
  92. HiC has 3577071 rows after windowing between 0 and 5000000
  93. process.hic: Elapsed time: 2.336911916732788
  94. HiC added to predictions table. Elapsed time: 1.619476079940796
  95. HiC Complete
  96. Completed chromosome: chr15. Elapsed time: 8.271932601928711
  97.  
  98. Making predictions for chromosome: chr11
  99. Making putative predictions table...
  100. Using: DIPG/input_data/HiC/raw/chr11/chr11.KRobserved.gz
  101. Begin HiC
  102. Loading HiC
  103. hic.to.sparse: Elapsed time: 3.418785572052002
  104. HiC Matrix has row sums of 1737.3676537735346, making doubly stochastic...
  105. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  106.   norms[norms < kr_cutoff] = np.nan
  107. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  108.   norms[norms >= kr_cutoff] = 1
  109. HiC has 5745287 rows after windowing between 0 and 5000000
  110. process.hic: Elapsed time: 3.9936869144439697
  111. HiC added to predictions table. Elapsed time: 3.0636868476867676
  112. HiC Complete
  113. Completed chromosome: chr11. Elapsed time: 14.807864904403687
  114.  
  115. Making predictions for chromosome: chr10
  116. Making putative predictions table...
  117. Using: DIPG/input_data/HiC/raw/chr10/chr10.KRobserved.gz
  118. Begin HiC
  119. Loading HiC
  120. hic.to.sparse: Elapsed time: 3.1262118816375732
  121. HiC Matrix has row sums of 1670.924667443995, making doubly stochastic...
  122. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  123.   norms[norms < kr_cutoff] = np.nan
  124. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  125.   norms[norms >= kr_cutoff] = 1
  126. HiC has 5630844 rows after windowing between 0 and 5000000
  127. process.hic: Elapsed time: 3.8438384532928467
  128. HiC added to predictions table. Elapsed time: 1.9274606704711914
  129. HiC Complete
  130. Completed chromosome: chr10. Elapsed time: 11.547400712966919
  131.  
  132. Making predictions for chromosome: chr13
  133. Making putative predictions table...
  134. Using: DIPG/input_data/HiC/raw/chr13/chr13.KRobserved.gz
  135. Begin HiC
  136. Loading HiC
  137. hic.to.sparse: Elapsed time: 1.5997390747070312
  138. HiC Matrix has row sums of 1003.5671665422119, making doubly stochastic...
  139. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  140.   norms[norms < kr_cutoff] = np.nan
  141. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  142.   norms[norms >= kr_cutoff] = 1
  143. HiC has 3150935 rows after windowing between 0 and 5000000
  144. process.hic: Elapsed time: 2.3841841220855713
  145. HiC added to predictions table. Elapsed time: 1.0804293155670166
  146. HiC Complete
  147. Completed chromosome: chr13. Elapsed time: 6.3783345222473145
  148.  
  149. Making predictions for chromosome: chrX
  150. Making putative predictions table...
  151. Using: DIPG/input_data/HiC/raw/chrX/chrX.KRobserved.gz
  152. Begin HiC
  153. Loading HiC
  154. hic.to.sparse: Elapsed time: 2.5769197940826416
  155. HiC Matrix has row sums of 916.6882453939974, making doubly stochastic...
  156. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  157.   norms[norms < kr_cutoff] = np.nan
  158. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  159.   norms[norms >= kr_cutoff] = 1
  160. HiC has 4555828 rows after windowing between 0 and 5000000
  161. process.hic: Elapsed time: 3.750195026397705
  162. HiC added to predictions table. Elapsed time: 1.2848665714263916
  163. HiC Complete
  164. Completed chromosome: chrX. Elapsed time: 9.126367330551147
  165.  
  166. Making predictions for chromosome: chr8
  167. Making putative predictions table...
  168. Using: DIPG/input_data/HiC/raw/chr8/chr8.KRobserved.gz
  169. Begin HiC
  170. Loading HiC
  171. hic.to.sparse: Elapsed time: 3.69053053855896
  172. HiC Matrix has row sums of 1576.284960351589, making doubly stochastic...
  173. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  174.   norms[norms < kr_cutoff] = np.nan
  175. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  176.   norms[norms >= kr_cutoff] = 1
  177. HiC has 6140784 rows after windowing between 0 and 5000000
  178. process.hic: Elapsed time: 4.3278648853302
  179. HiC added to predictions table. Elapsed time: 2.3899121284484863
  180. HiC Complete
  181. Completed chromosome: chr8. Elapsed time: 13.077553987503052
  182.  
  183. Making predictions for chromosome: chr3
  184. Making putative predictions table...
  185. Using: DIPG/input_data/HiC/raw/chr3/chr3.KRobserved.gz
  186. Begin HiC
  187. Loading HiC
  188. hic.to.sparse: Elapsed time: 4.709761619567871
  189. HiC Matrix has row sums of 1514.2904096524455, making doubly stochastic...
  190. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  191.   norms[norms < kr_cutoff] = np.nan
  192. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  193.   norms[norms >= kr_cutoff] = 1
  194. HiC has 8113923 rows after windowing between 0 and 5000000
  195. process.hic: Elapsed time: 5.709414005279541
  196. HiC added to predictions table. Elapsed time: 3.2483949661254883
  197. HiC Complete
  198. Completed chromosome: chr3. Elapsed time: 17.896188974380493
  199.  
  200. Making predictions for chromosome: chr5
  201. Making putative predictions table...
  202. Using: DIPG/input_data/HiC/raw/chr5/chr5.KRobserved.gz
  203. Begin HiC
  204. Loading HiC
  205. hic.to.sparse: Elapsed time: 4.56579065322876
  206. HiC Matrix has row sums of 1615.650225214133, making doubly stochastic...
  207. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  208.   norms[norms < kr_cutoff] = np.nan
  209. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  210.   norms[norms >= kr_cutoff] = 1
  211. HiC has 7965914 rows after windowing between 0 and 5000000
  212. process.hic: Elapsed time: 5.390728235244751
  213. HiC added to predictions table. Elapsed time: 2.989220142364502
  214. HiC Complete
  215. Completed chromosome: chr5. Elapsed time: 16.4359393119812
  216.  
  217. Making predictions for chromosome: chr19
  218. Making putative predictions table...
  219. Using: DIPG/input_data/HiC/raw/chr19/chr19.KRobserved.gz
  220. Begin HiC
  221. Loading HiC
  222. hic.to.sparse: Elapsed time: 1.1199641227722168
  223. HiC Matrix has row sums of 2118.1108999428952, making doubly stochastic...
  224. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  225.   norms[norms < kr_cutoff] = np.nan
  226. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  227.   norms[norms >= kr_cutoff] = 1
  228. HiC has 2536521 rows after windowing between 0 and 5000000
  229. process.hic: Elapsed time: 1.3841588497161865
  230. HiC added to predictions table. Elapsed time: 2.081949472427368
  231. HiC Complete
  232. Completed chromosome: chr19. Elapsed time: 8.21707820892334
  233.  
  234. Making predictions for chromosome: chr16
  235. Making putative predictions table...
  236. Using: DIPG/input_data/HiC/raw/chr16/chr16.KRobserved.gz
  237. Begin HiC
  238. Loading HiC
  239. hic.to.sparse: Elapsed time: 1.7209649085998535
  240. HiC Matrix has row sums of 1942.8680113256448, making doubly stochastic...
  241. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  242.   norms[norms < kr_cutoff] = np.nan
  243. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  244.   norms[norms >= kr_cutoff] = 1
  245. HiC has 3447195 rows after windowing between 0 and 5000000
  246. process.hic: Elapsed time: 2.1808383464813232
  247. HiC added to predictions table. Elapsed time: 1.6044023036956787
  248. HiC Complete
  249. Completed chromosome: chr16. Elapsed time: 7.981534719467163
  250.  
  251. Making predictions for chromosome: chr6
  252. Making putative predictions table...
  253. Using: DIPG/input_data/HiC/raw/chr6/chr6.KRobserved.gz
  254. Begin HiC
  255. Loading HiC
  256. hic.to.sparse: Elapsed time: 4.909979581832886
  257. HiC Matrix has row sums of 1962.3290202288767, making doubly stochastic...
  258. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  259.   norms[norms < kr_cutoff] = np.nan
  260. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  261.   norms[norms >= kr_cutoff] = 1
  262. HiC has 8114851 rows after windowing between 0 and 5000000
  263. process.hic: Elapsed time: 5.540345907211304
  264. HiC added to predictions table. Elapsed time: 3.1350207328796387
  265. HiC Complete
  266. Completed chromosome: chr6. Elapsed time: 17.704705238342285
  267.  
  268. Making predictions for chromosome: chr20
  269. Making putative predictions table...
  270. Using: DIPG/input_data/HiC/raw/chr20/chr20.KRobserved.gz
  271. Begin HiC
  272. Loading HiC
  273. hic.to.sparse: Elapsed time: 1.2047395706176758
  274. HiC Matrix has row sums of 1753.3570704479305, making doubly stochastic...
  275. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  276.   norms[norms < kr_cutoff] = np.nan
  277. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  278.   norms[norms >= kr_cutoff] = 1
  279. HiC has 2633551 rows after windowing between 0 and 5000000
  280. process.hic: Elapsed time: 1.494344711303711
  281. HiC added to predictions table. Elapsed time: 0.8540475368499756
  282. HiC Complete
  283. Completed chromosome: chr20. Elapsed time: 4.9600114822387695
  284.  
  285. Making predictions for chromosome: chr4
  286. Making putative predictions table...
  287. Using: DIPG/input_data/HiC/raw/chr4/chr4.KRobserved.gz
  288. Begin HiC
  289. Loading HiC
  290. hic.to.sparse: Elapsed time: 4.248570919036865
  291. HiC Matrix has row sums of 1297.3293834328256, making doubly stochastic...
  292. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  293.   norms[norms < kr_cutoff] = np.nan
  294. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  295.   norms[norms >= kr_cutoff] = 1
  296. HiC has 7397158 rows after windowing between 0 and 5000000
  297. process.hic: Elapsed time: 5.370730638504028
  298. HiC added to predictions table. Elapsed time: 2.310058832168579
  299. HiC Complete
  300. Completed chromosome: chr4. Elapsed time: 14.392668008804321
  301.  
  302. Making predictions for chromosome: chr1
  303. Making putative predictions table...
  304. Using: DIPG/input_data/HiC/raw/chr1/chr1.KRobserved.gz
  305. Begin HiC
  306. Loading HiC
  307. hic.to.sparse: Elapsed time: 7.181312084197998
  308. HiC Matrix has row sums of 2283.120313726259, making doubly stochastic...
  309. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  310.   norms[norms < kr_cutoff] = np.nan
  311. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  312.   norms[norms >= kr_cutoff] = 1
  313. HiC has 11009877 rows after windowing between 0 and 5000000
  314. process.hic: Elapsed time: 7.705347537994385
  315. HiC added to predictions table. Elapsed time: 5.269496917724609
  316. HiC Complete
  317. Completed chromosome: chr1. Elapsed time: 27.8169162273407
  318.  
  319. Making predictions for chromosome: chr14
  320. Making putative predictions table...
  321. Using: DIPG/input_data/HiC/raw/chr14/chr14.KRobserved.gz
  322. Begin HiC
  323. Loading HiC
  324. hic.to.sparse: Elapsed time: 1.5431585311889648
  325. HiC Matrix has row sums of 1156.8984891125122, making doubly stochastic...
  326. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  327.   norms[norms < kr_cutoff] = np.nan
  328. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  329.   norms[norms >= kr_cutoff] = 1
  330. HiC has 3049638 rows after windowing between 0 and 5000000
  331. process.hic: Elapsed time: 2.221566677093506
  332. HiC added to predictions table. Elapsed time: 1.5092990398406982
  333. HiC Complete
  334. Completed chromosome: chr14. Elapsed time: 7.424194097518921
  335.  
  336. Making predictions for chromosome: chr12
  337. Making putative predictions table...
  338. Using: DIPG/input_data/HiC/raw/chr12/chr12.KRobserved.gz
  339. Begin HiC
  340. Loading HiC
  341. hic.to.sparse: Elapsed time: 3.024580955505371
  342. HiC Matrix has row sums of 1634.3896941974212, making doubly stochastic...
  343. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  344.   norms[norms < kr_cutoff] = np.nan
  345. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  346.   norms[norms >= kr_cutoff] = 1
  347. HiC has 5678552 rows after windowing between 0 and 5000000
  348. process.hic: Elapsed time: 3.7780776023864746
  349. HiC added to predictions table. Elapsed time: 2.6896181106567383
  350. HiC Complete
  351. Completed chromosome: chr12. Elapsed time: 12.933283805847168
  352.  
  353. Making predictions for chromosome: chr21
  354. Making putative predictions table...
  355. Using: DIPG/input_data/HiC/raw/chr21/chr21.KRobserved.gz
  356. Begin HiC
  357. Loading HiC
  358. hic.to.sparse: Elapsed time: 0.6781599521636963
  359. HiC Matrix has row sums of 1812.4097497073167, making doubly stochastic...
  360. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  361.   norms[norms < kr_cutoff] = np.nan
  362. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  363.   norms[norms >= kr_cutoff] = 1
  364. HiC has 1668844 rows after windowing between 0 and 5000000
  365. process.hic: Elapsed time: 0.8591644763946533
  366. HiC added to predictions table. Elapsed time: 0.44057464599609375
  367. HiC Complete
  368. Completed chromosome: chr21. Elapsed time: 2.6194534301757812
  369.  
  370. Making predictions for chromosome: chr2
  371. Making putative predictions table...
  372. Using: DIPG/input_data/HiC/raw/chr2/chr2.KRobserved.gz
  373. Begin HiC
  374. Loading HiC
  375. hic.to.sparse: Elapsed time: 6.2712249755859375
  376. HiC Matrix has row sums of 1620.347024590508, making doubly stochastic...
  377. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:136: RuntimeWarning: invalid value encountered in less
  378.   norms[norms < kr_cutoff] = np.nan
  379. /home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py:137: RuntimeWarning: invalid value encountered in greater_equal
  380.   norms[norms >= kr_cutoff] = 1
  381. HiC has 10075298 rows after windowing between 0 and 5000000
  382. process.hic: Elapsed time: 7.429325819015503
  383. HiC added to predictions table. Elapsed time: 3.9282379150390625
  384. HiC Complete
  385. Completed chromosome: chr2. Elapsed time: 22.885234832763672
  386.  
  387. Making predictions for chromosome: chr9
  388. Making putative predictions table...
  389. Using: DIPG/input_data/HiC/raw/chr9/chr9.VCobserved.gz
  390. Begin HiC
  391. Loading HiC
  392. Traceback (most recent call last):
  393.   File "src/predict.py", line 141, in <module>
  394.     main()
  395.   File "src/predict.py", line 103, in main
  396.     this_chr = make_predictions(chromosome, this_enh, this_genes, args)
  397.   File "/home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/predictor.py", line 14, in make_predictions
  398.     pred = add_hic_to_enh_gene_table(enhancers, genes, pred, hic_file, hic_norm_file, hic_is_vc, chromosome, args)
  399.   File "/home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/predictor.py", line 63, in add_hic_to_enh_gene_table
  400.     gamma = args.hic_gamma)
  401.   File "/home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py", line 37, in load_hic
  402.     HiC_sparse_mat = hic_to_sparse(hic_file, hic_norm_file, hic_resolution)
  403.   File "/home/craig/Projects/DIPG/newpipeline/ABC-Enhancer-Gene-Prediction/src/hic.py", line 145, in hic_to_sparse
  404.     header=None, engine='c', memory_map=True)
  405.   File "/home/craig/.local/lib/python3.6/site-packages/pandas/io/parsers.py", line 685, in parser_f
  406.     return _read(filepath_or_buffer, kwds)
  407.   File "/home/craig/.local/lib/python3.6/site-packages/pandas/io/parsers.py", line 457, in _read
  408.     parser = TextFileReader(fp_or_buf, **kwds)
  409.   File "/home/craig/.local/lib/python3.6/site-packages/pandas/io/parsers.py", line 895, in __init__
  410.     self._make_engine(self.engine)
  411.   File "/home/craig/.local/lib/python3.6/site-packages/pandas/io/parsers.py", line 1135, in _make_engine
  412.     self._engine = CParserWrapper(self.f, **self.options)
  413.   File "/home/craig/.local/lib/python3.6/site-packages/pandas/io/parsers.py", line 1917, in __init__
  414.     self._reader = parsers.TextReader(src, **kwds)
  415.   File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.__cinit__
  416.   File "pandas/_libs/parsers.pyx", line 629, in pandas._libs.parsers.TextReader._setup_parser_source
  417.   File "/usr/lib/python3.6/gzip.py", line 163, in __init__
  418.     fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
  419. FileNotFoundError: [Errno 2] No such file or directory: 'DIPG/input_data/HiC/raw/chr9/chr9.VCobserved.gz'
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