error on angel_train.py, pickle not produced

[veravelasco]

Hi, Please let me know what this error is about? Its seems like some parts of the process for angel_train.py worked but ultimately there is no pickle produced. Thanks in advance.

/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Bio/Seq.py:2715: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. BiopythonWarning) running get_data_parallel for coding, chunk 0 launching all workers launching worker Process-1 launching worker Process-2 processing record PB.99.1|chr1:11796161-11810824(+)|i1a_c13849/f19p49/1138/RT|m.1, frame 0 launching worker Process-3 launching worker Process-4 Done with records processing record PB.99.2|chr1:11796161-11810824(+)|i1a_c1909/f68p136/1135/RT|m.2, frame 0 Process Process-1: Traceback (most recent call last): File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/lib64/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, self._kwargs) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/SmartORF.py", line 35, in add_data_worker processing record PB.99.4|chr1:11796161-11810824(+)|i1a_c49914/f6p67/1234/RT|m.4, frame 0 Process Process-2: Traceback (most recent call last): File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap Process Process-3: Traceback (most recent call last): File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/lib64/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, *self._kwargs) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/SmartORF.py", line 35, in add_data_worker self.run() File "/usr/lib64/python2.7/multiprocessing/process.py", line 114, in run self._target(self._args, self._kwargs) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/SmartORF.py", line 35, in add_data_worker stuff = ORFscores.make_data_smart(rec.seq, o_all, frame_shift=i) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/ORFscores.py", line 72, in make_data_smart stuff = ORFscores.make_data_smart(rec.seq, o_all, frame_shift=i) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/ORFscores.py", line 72, in make_data_smart arr = make_amino_scores(aa_freq)+make_diamino_scores(di_freq,o.diamino_range)+make_codon_scores(aa_freq,codon_freq) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/ORFscores.py", line 50, in make_codon_scores arr.append(aa_freq['']1./codon_freq[codon]) arr = make_amino_scores(aa_freq)+make_diamino_scores(di_freq,o.diamino_range)+make_codon_scores(aa_freq,codon_freq) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/ORFscores.py", line 50, in make_codon_scores arr.append(aa_freq['']1./codon_freq[codon]) ZeroDivisionError: float division by zero stuff = ORFscores.make_data_smart(rec.seq, o_all, frame_shift=i) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/ORFscores.py", line 72, in make_data_smart arr = make_amino_scores(aa_freq)+make_diamino_scores(di_freq,o.diamino_range)+make_codon_scores(aa_freq,codon_freq) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/ORFscores.py", line 50, in make_codon_scores arr.append(aa_freq['']1./codon_freq[codon]) ZeroDivisionError: float division by zero Traceback (most recent call last): File "/isg/shared/apps/angel/2.7/bin/angel_train.py", line 4, in import('pkg_resources').run_script('Angel==2.7', 'angel_train.py') File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/EGG-INFO/scripts/angel_train.py", line 17, in ANGEL_training(args.cds_filename, args.utr_filename, args.output_pickle, num_workers=args.cpus) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/SmartORF.py", line 100, in ANGEL_training data_pos = get_data_parallel(o_all, coding, [0], num_workers) File "/isg/shared/apps/angel/2.7/lib/python2.7/site-packages/Angel-2.7-py2.7-linux-x86_64.egg/Angel/SmartORF.py", line 65, in get_data_parallel obj = queue.get(timeout=60) File "/usr/lib64/python2.7/multiprocessing/queues.py", line 132, in get raise Empty

[Renxiaoliang]

Hi veravelasco, I have encountered the same problem with no ideas. Have you solved this?

[veravelasco]

Hi. No, I was not able to solve it. I just ended up using transedecoder.

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From: Renxiaoliang notifications@github.com Sent: Tuesday, May 12, 2020 10:42:03 PM To: PacificBiosciences/ANGEL ANGEL@noreply.github.com Cc: Vera Velasco vera.velasco@utoronto.ca; Author author@noreply.github.com Subject: Re: [PacificBiosciences/ANGEL] error on angel_train.py, pickle not produced (#32)

Hi veravelasco, I have encountered the same problem with no ideas. Have you solved this?

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