chapmanb
commented
7 years ago Thanks for the report and sorry about the issue. This looks like the same problem as #1590 and I believe @etal pushed a fix in CNVkit 0.8.1. Could you try updating to ensure you have the latest?
bcbio_conda install -c bioconda cnvkitand see if that resolves the problem? Thanks for helping debug and hope this gets your analysis completed.
phu5ion
Hi Brad,
I met a problem with running CNVkit using the bcbio pipeline. Looks to me like it's due to one of the helper scripts. Would you mind taking a look at it please? Thank you!
[2016-11-15T16:24Z] /mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py:3569: RuntimeWarning: Invalid value encountered in median [2016-11-15T16:24Z] RuntimeWarning) [2016-11-15T16:24Z] Segmented on allele freqs in 1:20502212-20880734 [2016-11-15T16:24Z] Segmented on allele freqs in 1:152101138-152329094 [2016-11-15T16:24Z] Segmented on allele freqs in 6:31948398-32053950 [2016-11-15T16:24Z] Segmented on allele freqs in 9:14748-21165524 [2016-11-15T16:24Z] Segmented on allele freqs in 9:33817744-34723732 [2016-11-15T16:24Z] Segmented on allele freqs in 9:71079943-84527890 [2016-11-15T16:24Z] Segmented on allele freqs in 11:65265219-65293234 [2016-11-15T16:24Z] Segmented on allele freqs in 12:9590547-9728325 [2016-11-15T16:24Z] Segmented on allele freqs in 12:52947518-133841395 [2016-11-15T16:24Z] Segmented on allele freqs in 16:2147288-2165682 [2016-11-15T16:24Z] Segmented on allele freqs in 19:11594210-11915395 [2016-11-15T16:24Z] Segmented on allele freqs in 19:19716614-24631282 [2016-11-15T16:24Z] Traceback (most recent call last): [2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/bin/cnvkit.py", line 13, in
[2016-11-15T16:24Z] args.func(args)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 726, in _cmd_segment
[2016-11-15T16:24Z] processes=args.processes)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 34, in do_segmentation
[2016-11-15T16:24Z] save_dataframe, rlibpath)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 130, in _do_segmentation
[2016-11-15T16:24Z] transfer_fields(segarr, cnarr)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 179, in transfer_fields
[2016-11-15T16:24Z] segweights[i] = subprobes['weight'].sum()
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", line 130, in getitem
[2016-11-15T16:24Z] return self.data[index]
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 1997, in getitem
[2016-11-15T16:24Z] return self._getitem_column(key)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2004, in _getitem_column
[2016-11-15T16:24Z] return self._get_item_cache(key)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1350, in _get_item_cache
[2016-11-15T16:24Z] values = self._data.get(item)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3290, in get
[2016-11-15T16:24Z] loc = self.items.get_loc(item)
[2016-11-15T16:24Z] File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/indexes/base.py", line 1947, in get_loc
[2016-11-15T16:24Z] return self._engine.get_loc(self._maybe_cast_indexer(key))
[2016-11-15T16:24Z] File "pandas/index.pyx", line 137, in pandas.index.IndexEngine.get_loc (pandas/index.c:4154)
[2016-11-15T16:24Z] File "pandas/index.pyx", line 159, in pandas.index.IndexEngine.get_loc (pandas/index.c:4018)
[2016-11-15T16:24Z] File "pandas/hashtable.pyx", line 675, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12368)
[2016-11-15T16:24Z] File "pandas/hashtable.pyx", line 683, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12322)
[2016-11-15T16:24Z] KeyError: 'weight'
[2016-11-15T16:24Z] Uncaught exception occurred
Traceback (most recent call last):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; unset R_HOME && export PATH=/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/bin:$PATH && /mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/bin/cnvkit.py segment -o /mnt/projects/dlho/tancrc/Plasma_exome/analysis/work/structural/T180_baseline/cnvkit/raw/tx/tmp6P3yTH/T180_baseline-sort.cns /mnt/projects/dlho/tancrc/Plasma_exome/analysis/work/structural/T180_baseline/cnvkit/raw/T180_baseline-sort.cnr -v /mnt/projects/dlho/tancrc/Plasma_exome/analysis/work/freebayes/T0-vepeffects-annotated-filter.vcf.gz
Loaded 69466 records; skipped: 1170 somatic, 0 depth
Selected test sample T180_baseline and control sample N180_WBC
Dropped 33 outlier bins:
chromosome start end gene log2 depth \
0 1 47799580 47799822 CMPK1 -23.4239 0.0
1 1 94374574 94374776 GCLM -23.3657 0.0
2 2 88926422 88926637 EIF2AK3 -23.5664 0.0
3 2 99439265 99439513 KIAA1211L -23.3389 0.0
4 2 174828462 174828664 SP3 -23.5508 0.0
5 2 220313475 220313739 SPEG -23.1710 0.0
6 2 239229242 239229455 TRAF3IP1 -23.3195 0.0
7 3 9439106 9439397 SETD5,SETD5-AS1 -23.0782 0.0
8 3 50313698 50313931 SEMA3B -23.3550 0.0
9 3 195163447 195163649 ACAP2 -23.5964 0.0
10 7 73498296 73498432 LIMK1 -23.4877 0.0
11 11 67071067 67071189 SSH3 -23.3575 0.0
12 12 9067292 9067423 PHC1 -23.3060 0.0
13 13 37393394 37393639 RFXAP -23.4086 0.0
14 15 38856749 38856871 RASGRP1 -23.6216 0.0
15 16 718319 718441 RHOT2 -23.5570 0.0
16 16 730482 730694 STUB1 -23.4402 0.0
17 16 15005072 15005174 MIR3180-1,hsa-mir-3180-3 -23.7579 0.0
18 16 89642270 89642512 CPNE7 -23.3488 0.0
19 16 89989786 89989928 TUBB3 -23.3175 0.0
0 0.157922 1 0.163452 2 0.287465 3 0.144785 4 0.276951 5 0.145293 6 0.131580 7 0.124337 8 0.155783 9 0.290737 10 0.187469 11 0.122643 12 0.082347 13 0.257050 14 0.271211 15 0.272108 16 0.213426 17 0.318241 18 0.136248 19 0.101492 ... /mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py:3569: RuntimeWarning: Invalid value encountered in median RuntimeWarning) Segmented on allele freqs in 1:20502212-20880734 Segmented on allele freqs in 1:152101138-152329094 Segmented on allele freqs in 6:31948398-32053950 Segmented on allele freqs in 9:14748-21165524 Segmented on allele freqs in 9:33817744-34723732 Segmented on allele freqs in 9:71079943-84527890 Segmented on allele freqs in 11:65265219-65293234 Segmented on allele freqs in 12:9590547-9728325 Segmented on allele freqs in 12:52947518-133841395 Segmented on allele freqs in 16:2147288-2165682 Segmented on allele freqs in 19:11594210-11915395 Segmented on allele freqs in 19:19716614-24631282 Traceback (most recent call last): File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/bin/cnvkit.py", line 13, in
args.func(args)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 726, in _cmd_segment
processes=args.processes)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 34, in do_segmentation
save_dataframe, rlibpath)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 130, in _do_segmentation
transfer_fields(segarr, cnarr)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 179, in transfer_fields
segweights[i] = subprobes['weight'].sum()
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", line 130, in getitem
return self.data[index]
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 1997, in getitem
return self._getitem_column(key)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2004, in _getitem_column
return self._get_item_cache(key)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1350, in _get_item_cache
values = self._data.get(item)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3290, in get
loc = self.items.get_loc(item)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/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'
' returned non-zero exit status 1
Traceback (most recent call last):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/bin/bcbio_nextgen.py", line 230, in
main(kwargs)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/bin/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 176, in variant2pipeline
samples = structural.run(samples, run_parallel, "initial")
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/structural/init.py", line 146, in run
for xs in to_process.values()))
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(*args, kwargs) for func, args, kwargs in self.items]
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, *args, kwargs)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 228, in detect_sv
return structural.detect_sv(args)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/structural/init.py", line 165, in detect_sv
for svdata in caller_fn(items):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 29, in run
return _cnvkit_by_type(items, background)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 41, in _cnvkit_by_type
return _run_cnvkit_cancer(items, background)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 85, in _run_cnvkit_cancer
ckouts = _run_cnvkit_shared([paired.tumor_data], normal_data)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 167, in _run_cnvkit_shared
inputs[0]["config"], parallel)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(args, kwargs) for func, args, kwargs in self.items]
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, *args, kwargs)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 63, in wrapper
out = f(*args, **kwargs)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 201, in _cnvkit_segment
do.run(export_cmd + " ".join(cmd), "CNVkit segment")
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; unset R_HOME && export PATH=/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/bin:$PATH && /mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/bin/cnvkit.py segment -o /mnt/projects/dlho/tancrc/Plasma_exome/analysis/work/structural/T180_baseline/cnvkit/raw/tx/tmp6P3yTH/T180_baseline-sort.cns /mnt/projects/dlho/tancrc/Plasma_exome/analysis/work/structural/T180_baseline/cnvkit/raw/T180_baseline-sort.cnr -v /mnt/projects/dlho/tancrc/Plasma_exome/analysis/work/freebayes/T0-vepeffects-annotated-filter.vcf.gz
Loaded 69466 records; skipped: 1170 somatic, 0 depth
Selected test sample T180_baseline and control sample N180_WBC
Dropped 33 outlier bins:
chromosome start end gene log2 depth \
0 1 47799580 47799822 CMPK1 -23.4239 0.0
1 1 94374574 94374776 GCLM -23.3657 0.0
2 2 88926422 88926637 EIF2AK3 -23.5664 0.0
3 2 99439265 99439513 KIAA1211L -23.3389 0.0
4 2 174828462 174828664 SP3 -23.5508 0.0
5 2 220313475 220313739 SPEG -23.1710 0.0
6 2 239229242 239229455 TRAF3IP1 -23.3195 0.0
7 3 9439106 9439397 SETD5,SETD5-AS1 -23.0782 0.0
8 3 50313698 50313931 SEMA3B -23.3550 0.0
9 3 195163447 195163649 ACAP2 -23.5964 0.0
10 7 73498296 73498432 LIMK1 -23.4877 0.0
11 11 67071067 67071189 SSH3 -23.3575 0.0
12 12 9067292 9067423 PHC1 -23.3060 0.0
13 13 37393394 37393639 RFXAP -23.4086 0.0
14 15 38856749 38856871 RASGRP1 -23.6216 0.0
15 16 718319 718441 RHOT2 -23.5570 0.0
16 16 730482 730694 STUB1 -23.4402 0.0
17 16 15005072 15005174 MIR3180-1,hsa-mir-3180-3 -23.7579 0.0
18 16 89642270 89642512 CPNE7 -23.3488 0.0
19 16 89989786 89989928 TUBB3 -23.3175 0.0
0 0.157922 1 0.163452 2 0.287465 3 0.144785 4 0.276951 5 0.145293 6 0.131580 7 0.124337 8 0.155783 9 0.290737 10 0.187469 11 0.122643 12 0.082347 13 0.257050 14 0.271211 15 0.272108 16 0.213426 17 0.318241 18 0.136248 19 0.101492 ... /mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py:3569: RuntimeWarning: Invalid value encountered in median RuntimeWarning) Segmented on allele freqs in 1:20502212-20880734 Segmented on allele freqs in 1:152101138-152329094 Segmented on allele freqs in 6:31948398-32053950 Segmented on allele freqs in 9:14748-21165524 Segmented on allele freqs in 9:33817744-34723732 Segmented on allele freqs in 9:71079943-84527890 Segmented on allele freqs in 11:65265219-65293234 Segmented on allele freqs in 12:9590547-9728325 Segmented on allele freqs in 12:52947518-133841395 Segmented on allele freqs in 16:2147288-2165682 Segmented on allele freqs in 19:11594210-11915395 Segmented on allele freqs in 19:19716614-24631282 Traceback (most recent call last): File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/bin/cnvkit.py", line 13, in
args.func(args)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 726, in _cmd_segment
processes=args.processes)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 34, in do_segmentation
save_dataframe, rlibpath)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 130, in _do_segmentation
transfer_fields(segarr, cnarr)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/segmentation/init.py", line 179, in transfer_fields
segweights[i] = subprobes['weight'].sum()
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", line 130, in getitem
return self.data[index]
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 1997, in getitem
return self._getitem_column(key)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2004, in _getitem_column
return self._get_item_cache(key)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1350, in _get_item_cache
values = self._data.get(item)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3290, in get
loc = self.items.get_loc(item)
File "/mnt/projects/dlho/tancrc/bcbio_pipeline/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'
' returned non-zero exit status 1