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tkoomar/cnvkit_segment.log Secret

Created October 7, 2016 22:46
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Standard error produced by cnvkit segment during a bcbio run
Raw
cnvkit_segment.log
Loaded 4100275 records; skipped: 0 somatic, 0 depth
Selected test sample sample51 and control sample
Dropped 26 outlier bins:
chromosome start end \
0 1 869718 870218
1 1 68008231 68008729
2 1 149569343 149569842
3 1 187465970 187466464
4 2 33092250 33092750
5 3 32807115 32807615
6 3 194555759 194556263
7 5 55429558 55430058
8 5 127172638 127173136
9 6 18402131 18402631
10 6 32779058 32779559
11 9 33213364 33213865
12 9 70506739 70507240
13 9 104219775 104220275
14 9 131701261 131701761
15 9 132026790 132027295
16 9 138479318 138479818
17 10 18503091 18503591
18 10 107950984 107951484
19 11 65643013 65643513
gene log2 depth \
0 AGRN,AL645608.1,C1orf159,C1orf170,HES4,ISG15,K... -5.23558 0.890000
1 RNU6-1031P,RP11-393N21.1,RP4-763G1.2 -24.42100 0.000000
2 AL358813.1,AL358813.2,FAM231D,RNU1-68P,RNVU1-2... -24.41080 0.000000
3 RP11-445P19.2 -7.45399 0.121457
4 LINC00486 -24.30190 0.000000
5 AC139452.2,CNOT10,CNOT10-AS1,SUGT1P2 -24.39030 0.000000
6 AC090505.1 -7.93729 0.111111
7 ANKRD55,RNA5SP184,RNU6-299P,RP11-365H8.2,RPL17P22 -24.30820 0.000000
8 CTC-228N24.1,CTC-228N24.2 -24.37660 0.000000
9 RNF144B,RP11-528A10.1,RP11-528A10.2,snoU13 -24.38800 0.000000
10 HLA-DOB,HLA-Z,PPP1R2P1,PSMB8,PSMB9,TAP1,TAP2,T... -24.45520 0.000000
11 AQP7,BAG1,CHMP5,NFX1,RP11-311H10.4,SPINK4,Y_RNA -24.49410 0.000000
12 CBWD5,FOXD4L4 -24.30200 0.000000
13 AL591377.1,ALDOB,BAAT,BAATP1,FYTTD1P1,GRIN3A,L... -24.35910 0.000000
14 AL158151.2,AL359091.1,AL359091.2,AL590708.1,AL... -24.62780 0.000000
15 RP11-344B5.3,RP11-344B5.4 -24.64850 0.000000
16 AL161452.1,C9orf116,LCN1,MRPS2,OBP2A,PAEP,PPP1... -25.04840 0.000000
17 CACNB2,NSUN6,RP11-109I13.2,RP11-383B4.4,RP11-4... -6.97636 0.172000
18 RP11-298H24.1 -24.37430 0.000000
19 C11orf68,CCDC85B,CFL1,CTSW,DRAP1,EFEMP2,FIBP,F... -24.54220 0.000000
weight
0 0.676590
1 0.673884
2 0.675237
3 0.668471
4 0.676590
5 0.676590
6 0.682003
7 0.676590
8 0.673884
9 0.676590
10 0.677943
11 0.677943
12 0.677943
13 0.676590
14 0.676590
15 0.683356
16 0.676590
17 0.676590
18 0.676590
19 0.676590
...
Segmented on allele freqs in 1:2241287-2254288
Segmented on allele freqs in 1:13438112-13472661
Segmented on allele freqs in 1:13477643-13536943
Segmented on allele freqs in 1:13638389-13646412
Segmented on allele freqs in 1:17998434-18064484
Segmented on allele freqs in 1:40832508-40836008
Segmented on allele freqs in 1:89475571-89479073
Segmented on allele freqs in 1:110227026-110244531
Segmented on allele freqs in 1:144079213-144095852
Segmented on allele freqs in 1:144274400-144301351
Segmented on allele freqs in 1:146307551-146390552
Segmented on allele freqs in 1:147551859-147604814
Segmented on allele freqs in 1:147604813-147704228
Segmented on allele freqs in 1:147869872-147912408
Segmented on allele freqs in 1:148601021-148623571
Segmented on allele freqs in 1:196188409-196194913
Segmented on allele freqs in 1:206128298-206147844
Segmented on allele freqs in 1:207700103-207744620
Segmented on allele freqs in 1:223725360-223747873
Segmented on allele freqs in 1:246858625-246883350
Segmented on allele freqs in 2:1706631-1708132
Segmented on allele freqs in 2:16329582-16334619
Segmented on allele freqs in 2:90284373-90310401
Segmented on allele freqs in 2:243088810-243102807
Segmented on allele freqs in 2:243161345-243170824
Segmented on allele freqs in 3:129763380-129799712
Segmented on allele freqs in 3:142836178-142841691
Segmented on allele freqs in 4:33848705-33857197
Segmented on allele freqs in 4:75281143-75323213
Segmented on allele freqs in 5:68831347-68899845
Segmented on allele freqs in 5:68899844-68946343
Segmented on allele freqs in 5:70060444-70085935
Segmented on allele freqs in 5:70085934-70105428
Segmented on allele freqs in 5:70110425-70122922
Segmented on allele freqs in 5:70509584-70533092
Segmented on allele freqs in 5:78463091-78494540
Segmented on allele freqs in 5:175412377-175424869
Segmented on allele freqs in 5:177226174-177236175
Segmented on allele freqs in 5:177329681-177338183
Segmented on allele freqs in 6:31422172-31424673
Segmented on allele freqs in 6:132019122-132034605
Segmented on allele freqs in 7:16829114-16830613
Segmented on allele freqs in 7:72492251-72582215
Segmented on allele freqs in 7:74544896-74553900
Segmented on allele freqs in 7:76163238-76169242
Segmented on allele freqs in 7:100619404-100637928
Segmented on allele freqs in 7:136519357-136521870
Segmented on allele freqs in 7:143397459-143420484
Segmented on allele freqs in 7:143550765-143576777
Segmented on allele freqs in 8:101570-124545
Segmented on allele freqs in 8:6503638-6549656
Segmented on allele freqs in 8:7018071-7026653
Segmented on allele freqs in 8:7803343-7873310
Segmented on allele freqs in 8:7873309-7879807
Segmented on allele freqs in 8:12206517-12233494
Segmented on allele freqs in 8:12235491-12251477
Segmented on allele freqs in 8:35386267-35389788
Segmented on allele freqs in 8:37334422-37383903
Segmented on allele freqs in 8:74381272-74476829
Segmented on allele freqs in 8:86554900-86556392
Segmented on allele freqs in 9:39260803-39399278
Segmented on allele freqs in 9:39444360-39472012
Segmented on allele freqs in 9:39472011-39492368
Segmented on allele freqs in 9:40798375-40818392
Segmented on allele freqs in 9:40818391-40838408
Segmented on allele freqs in 9:42719806-42755328
Segmented on allele freqs in 9:43064426-43127419
Segmented on allele freqs in 9:44411449-44473971
Segmented on allele freqs in 9:44473970-44676889
Segmented on allele freqs in 9:46999708-47009706
Segmented on allele freqs in 9:97105289-97109291
Segmented on allele freqs in 9:138931332-138947315
Segmented on allele freqs in 9:141121999-141124005
Segmented on allele freqs in 10:31117653-31246782
Segmented on allele freqs in 10:46371106-46560475
Segmented on allele freqs in 10:48726873-48744889
Segmented on allele freqs in 10:51596590-51605590
Segmented on allele freqs in 10:51836557-51847057
Segmented on allele freqs in 10:51902548-52000562
Segmented on allele freqs in 10:102027254-102068734
Segmented on allele freqs in 11:4968335-4976833
Segmented on allele freqs in 11:55431728-55457653
Segmented on allele freqs in 12:6040389-6041891
Segmented on allele freqs in 12:129572596-129574087
Segmented on allele freqs in 15:21312735-21318466
Segmented on allele freqs in 15:23673463-23678948
Segmented on allele freqs in 15:28661636-28668167
Segmented on allele freqs in 15:83181855-83213852
Segmented on allele freqs in 15:102310961-102327974
Segmented on allele freqs in 15:102432756-102445801
Segmented on allele freqs in 16:15200398-15206397
Segmented on allele freqs in 16:15206396-15239885
Segmented on allele freqs in 16:21779042-21808412
Segmented on allele freqs in 16:21808411-21849400
Segmented on allele freqs in 16:21849399-21877392
Segmented on allele freqs in 16:21877391-21941374
Segmented on allele freqs in 16:28683604-28722605
Segmented on allele freqs in 16:90173587-90184588
Segmented on allele freqs in 17:5625588-5631531
Segmented on allele freqs in 17:34593535-34651846
Segmented on allele freqs in 17:36323638-36333158
Segmented on allele freqs in 17:75992746-76103181
Segmented on allele freqs in 17:76282073-76283573
Segmented on allele freqs in 17:76416376-76450397
Segmented on allele freqs in 17:77462714-77623550
Segmented on allele freqs in 19:843093-863094
Segmented on allele freqs in 19:8793868-8851875
Segmented on allele freqs in 19:55307346-55329840
Segmented on allele freqs in 19:56241253-56264380
Segmented on allele freqs in 21:11000029-11007527
Segmented on allele freqs in 21:11007526-11020521
Segmented on allele freqs in 21:15140596-15192721
Segmented on allele freqs in 22:21516539-21520034
Segmented on allele freqs in X:49176492-49211495
Segmented on allele freqs in X:72068157-72164174
Segmented on allele freqs in X:129309442-129652186
Segmented on allele freqs in X:154588770-154715080
Traceback (most recent call last):
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/bin/cnvkit.py", line 13, in <module>
args.func(args)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 726, in _cmd_segment
processes=args.processes)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/__init__.py", line 34, in do_segmentation
save_dataframe, rlibpath)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/__init__.py", line 130, in _do_segmentation
transfer_fields(segarr, cnarr)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/__init__.py", line 179, in transfer_fields
segweights[i] = subprobes['weight'].sum()
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", line 130, in __getitem__
return self.data[index]
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 1997, in __getitem__
return self._getitem_column(key)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2004, in _getitem_column
return self._get_item_cache(key)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1350, in _get_item_cache
values = self._data.get(item)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3290, in get
loc = self.items.get_loc(item)
File "/Dedicated/jmichaelson-wdata/bcbio/anaconda/lib/python2.7/site-packages/pandas/indexes/base.py", line 1947, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/index.pyx", line 137, in pandas.index.IndexEngine.get_loc (pandas/index.c:4154)
File "pandas/index.pyx", line 159, in pandas.index.IndexEngine.get_loc (pandas/index.c:4018)
File "pandas/hashtable.pyx", line 675, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12368)
File "pandas/hashtable.pyx", line 683, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12322)
KeyError: 'weight'
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