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problem with recapseg tumor_pcov

Hello
I would like to ask the error of recapseg tumor_pcov. I run the script with virtualenv as recommend by installation process.I've got partial output file (target file with error in 'name' column) except segment file.
I don't know is the problem related with bed file.. I try to follow the format of bed file, only difference in 'chr'.
Thanks if anyone could recommend.

here is my target file;
name contig start stop RS122003_T
0 chr1 69089 70009 0.09488382185788069
1 chr1 762078 762903 -0.021678666557854512
2 chr1 880430 880532 -0.11490885088311573
3 chr1 880896 881034 -0.24256055375794858

here is my bed file;
chr1 30366 30503 target_1_DKFZp434K1323
chr1 35105 35205 target_2_FAM138A
chr1 69089 70009 target_3_COSM75742

here is my error;
2015-12-23 10:04:59,175 INFO [capseg.tools.recapseg.recapseg:212] Version: 1.4.4.0
2015-12-23 10:04:59,175 INFO [capseg.tools.recapseg.recapseg:213] Args: Namespace(baits_file='Intersect_Ion&TargetSeg_hg19_correct.bed', case_cr_stat_list_file='/home/ubuntu/data/case_cr_stat_list_file', case_pcov_list_file='/home/ubuntu/data/case_pcov_list_file', case_sample_name_list_file='/home/ubuntu/data/case_sample_id_list', func=, is_debug=False, is_plotting=True, log_name='recapseg.log', no_pon_reduction=True, output_base_filename='/home/ubuntu/data/test_out', panel_data_file='/home/ubuntu/data/BAC_PON_test')
2015-12-23 10:04:59,175 INFO [capseg.tools.recapseg.recapseg:214] Log file: /home/ubuntu/data/recapseg.log
2015-12-23 10:04:59,175 INFO [capseg.tools.recapseg.recapseg:63] Running tumor pcov samples against panel of normals: Namespace(baits_file='Intersect_Ion&TargetSeg_hg19_correct.bed', case_cr_stat_list_file='/home/ubuntu/data/case_cr_stat_list_file', case_pcov_list_file='/home/ubuntu/data/case_pcov_list_file', case_sample_name_list_file='/home/ubuntu/data/case_sample_id_list', func=, is_debug=False, is_plotting=True, log_name='recapseg.log', no_pon_reduction=True, output_base_filename='/home/ubuntu/data/test_out', panel_data_file='/home/ubuntu/data/BAC_PON_test')
2015-12-23 10:04:59,176 INFO [capseg.Capsegger:218] Looping through file lists and creating file tuples
2015-12-23 10:04:59,176 INFO [capseg.Capsegger:223] 1 file tuples (samples) created.
2015-12-23 10:04:59,176 INFO [capseg.Capsegger:225] Looping through file tuples and creating list of proportional coverage data frames.
2015-12-23 10:04:59,178 INFO [capseg.Capsegger:231] Processed 1/1 file tuples.
2015-12-23 10:04:59,179 INFO [capseg.Capsegger:232] Processed 1/1 file tuples.
2015-12-23 10:04:59,179 INFO [capseg.panel.PanelDataFactory:37] Retrieving panel of normals from /home/ubuntu/data/BAC_PON_test
2015-12-23 10:04:59,343 INFO [capseg.panel.PanelDataFactory:49] Panel of normals loaded -- based on 141238 targets and 2 samples.
2015-12-23 10:04:59,395 INFO [capseg.Capsegger:326] RAM usage after panel loading: 174 MB
2015-12-23 10:04:59,395 INFO [capseg.filter.FilterNormalizer:70] RG filtering cases
2015-12-23 10:04:59,396 INFO [capseg.filter.FilterNormalizer:76] Target filtering cases
2015-12-23 10:04:59,396 INFO [capseg.filter.FilterNormalizer:43] Filter normalizing RS122003_T (1/1)
2015-12-23 10:04:59,606 INFO [capseg.filter.FilterNormalizer:47] RAM usage after loading dataframe: 206 MB
2015-12-23 10:05:04,938 INFO [capseg.filter.FilterNormalizer:65] RAM usage after freeing dataframe: 211 MB
2015-12-23 10:05:04,938 INFO [capseg.filter.FilterNormalizer:79] Done target filtering cases
2015-12-23 10:05:04,990 INFO [capseg.filter.FilterNormalizer:81] RAM usage after target-filtering cases: 211 MB
2015-12-23 10:05:05,251 INFO [capseg.Capsegger:260] Running tangent normalization...
2015-12-23 10:05:05,432 INFO [capseg.Capsegger:159] RAM usage before creating prenormalized data: 248 MB
2015-12-23 10:05:05,432 INFO [capseg.normalize.TangentNormalizer:28] Calculating target intersection of samples
2015-12-23 10:05:05,644 INFO [capseg.normalize.TangentNormalizer:44] Calculating initial block normalization
2015-12-23 10:05:05,699 INFO [capseg.Capsegger:161] RAM usage after creating prenormalized data: 247 MB
2015-12-23 10:05:05,699 INFO [capseg.Capsegger:164] Performing tangent normalization with reduced PoN
2015-12-23 10:05:05,768 INFO [capseg.normalize.TangentNormalizer:93] RAM usage at start of tn: 256 MB
2015-12-23 10:05:05,820 INFO [capseg.normalize.TangentNormalizer:96] RAM usage: 256 MB
2015-12-23 10:05:05,887 INFO [capseg.normalize.TangentNormalizer:106] RAM usage after processing tumors: 256 MB
2015-12-23 10:05:05,939 INFO [capseg.Capsegger:177] RAM usage after tangent normalization: 256 MB
2015-12-23 10:05:06,546 INFO [capseg.normalize.TangentNormalizer:61] Delta Copy-Qc = -0.00227580578264
2015-12-23 10:05:16,669 INFO [capseg.Capsegger:266] Beginning segmentation on any case samples...
2015-12-23 10:05:17,314 INFO [capseg.Capsegger:47] Found 1 sample(s) for segmentation: RS122003_T
['contig', 'start', 'stop', 'RS122003_T']
Analyzing: RS122003_T
Traceback (most recent call last):
File "/usr/local/bin/recapseg", line 9, in
load_entry_point('recapseg==1.4.4.0', 'console_scripts', 'recapseg')()
File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg/tools/recapseg/recapseg.py", line 217, in main
args.func(args)
File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg/tools/recapseg/recapseg.py", line 75, in process_tumor_pcov
args.baits_file, args.output_base_filename, args.is_plotting, is_using_reduced_pon=args.no_pon_reduction)
File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg/Capsegger.py", line 335, in run_tumor_pcov
output_base_filename, is_plotting, is_using_reduced_pon)
File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg/Capsegger.py", line 270, in _tn_and_segment
self._run_segmenter_on_df(normalized_df, output_base_filename, is_plotting)
File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg/Capsegger.py", line 50, in _run_segmenter_on_df
segment_data_frame = segmenter.input_and_segment_data(input_data_frame, sample_name)
File "/usr/local/lib/python2.7/dist-packages/recapseg-1.4.4.0-py2.7.egg/capseg/segment/Segmenter.py", line 47, in input_and_segment_data
pandas_result = pandas2ri.ri2pandas(result[result.names.index("output")])
File "/usr/lib/python2.7/dist-packages/rpy2/robjects/pandas2ri.py", line 63, in ri2pandas
raise NotImplementedError("Conversion from rpy2 DataFrame to pandas' DataFrame")
NotImplementedError: Conversion from rpy2 DataFrame to pandas' DataFrame
Closing remaining open files:/home/ubuntu/data/BAC_PON_test...done/home/ubuntu/data/BAC_PON_test...done/home/ubuntu/data/BAC_PON_test...done> ![](> > )

Issue · Github
by Sheila

Issue Number
444
State
closed
Last Updated
Milestone
Array
Closed By
vdauwera

Answers

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