roestlab / pyprophet Goto Github PK

incorrect startxref pointer(3)
incorrect startxref pointer(3)
Traceback (most recent call last):
  File "/home/mgh/python_ENV/bin/pyprophet", line 8, in <module>
    sys.exit(cli())
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/click/core.py", line 1289, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/main.py", line 112, in score
    PyProphetLearner(infile, outfile, classifier, xgb_hyperparams, xgb_params, xgb_params_space, xeval_fraction, xeval_num_iter, ss_initial_fdr, ss_iteration_fdr, ss_num_iter, ss_main_score, group_id, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0, lfdr_truncate, lfdr_monotone, lfdr_transformation, lfdr_adj, lfdr_eps, level, ipf_max_peakgroup_rank, ipf_max_peakgroup_pep, ipf_max_transition_isotope_overlap, ipf_min_transition_sn, tric_chromprob, threads, test, ss_score_filter, color_palette, main_score_selection_report).run()
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/runner.py", line 265, in run
    (result, scorer, weights) = self.run_algo()
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/runner.py", line 427, in run_algo
    (result, scorer, weights) = PyProphet(self.classifier, self.xgb_hyperparams, self.xgb_params, self.xgb_params_space, self.xeval_fraction, self.xeval_num_iter, self.ss_initial_fdr, self.ss_iteration_fdr, self.ss_num_iter, self.group_id, self.parametric, self.pfdr, self.pi0_lambda, self.pi0_method, self.pi0_smooth_df, self.pi0_smooth_log_pi0, self.lfdr_truncate, self.lfdr_monotone, self.lfdr_transformation, self.lfdr_adj, self.lfdr_eps, self.tric_chromprob, self.threads, self.test, self.ss_score_filter, self.color_palette, self.main_score_selection_report, self.outfile, self.level, self.ss_use_dynamic_main_score).learn_and_apply(self.table)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/pyprophet.py", line 259, in learn_and_apply
    result, scorer, trained_weights = self._learn_and_apply(table)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/pyprophet.py", line 267, in _learn_and_apply
    final_classifier = self._learn(experiment, score_columns)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/pyprophet.py", line 288, in _learn
    (ttt_scores, ttd_scores, w) = learner.learn_randomized(experiment, score_columns, 1)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/semi_supervised.py", line 44, in learn_randomized
    params, clf_scores, use_as_main_score = self.start_semi_supervised_learning(train, score_columns, working_thread_number)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/semi_supervised.py", line 170, in start_semi_supervised_learning
    td_peaks, bt_peaks = self.select_train_peaks(train, use_as_main_col_alias, self.ss_initial_fdr, self.parametric, self.pfdr, self.pi0_lambda, self.pi0_method, self.pi0_smooth_df, self.pi0_smooth_log_pi0, mapper, self.main_score_selection_report, self.outfile, self.level, working_thread_number)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/semi_supervised.py", line 139, in select_train_peaks
    cutoff = find_cutoff(tt_scores, td_scores, cutoff_fdr, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0, sel_column, mapper, main_score_selection_report, outfile, level, working_thread_number)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/stats.py", line 492, in find_cutoff
    error_stat, pi0 = error_statistics(tt_scores, td_scores, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0, False, sel_column=sel_column, mapper=mapper, save_report=main_score_selection_report, title=outfile, level=level, working_thread_number=working_thread_number)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/stats.py", line 466, in error_statistics
    main_score_selection_report(os.path.basename(title), sel_column, mapper, decoy_scores, target_scores, target_pvalues, pi0, pdf_path=os.path.join(os.path.dirname(title), os.path.splitext(os.path.basename(title))[0] + f"_main_score_selection_{level}_report_thread_{working_thread_number}.pdf"), worker_num=working_thread_number)
  File "/home/mgh/python_ENV/lib/python3.8/site-packages/pyprophet/report.py", line 208, in main_score_selection_report
    os.remove(temp_pdf_path)
FileNotFoundError: [Errno 2] No such file or directory: 'temp_main_score_selection_report_thread__1.pdf'