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JoseBlanca / seq_crumbs

Little sequence file utilities meant to work within Unix pipelines
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Filter_by_bowtie2 #7

Open ConradStack opened 10 years ago

ConradStack commented 10 years ago

I've having an issue running this "crumb". Specifically, the program is failing open SAM/BAM files:

<type 'exceptions.ValueError'> Python 2.7.5: /usr/bin/python Thu Feb 27 16:11:25 2014

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

/Library/Python/2.7/site-packages/crumbs/utils/bin_utils.py in main(funct=) 59 if fail: 60 raise RuntimeError('Generating a test error') 61 return(funct()) 62 except FileNotFoundError, error: 63 stderr.write(str(error) + '\n') funct =

/Users/conrad/utils/bin/filter_by_bowtie2 in filter_by_bowtie2() 77 78 write_filter_packets(passed_fhand, filtered_fhand, filter_packets, 79 args['out_format'], workers=workers) 80 flush_fhand(passed_fhand) 81 if filtered_fhand is not None: args = {'fail_drags_pair': True, 'filtered_fhand': <open file 'lane6_11.vectorhit.fastq', mode 'wt'>, 'in_fhands': [<open file 'tcacao_lane6_11_GGCTAC.fastq', mode 'rt'>], 'index': '/Users/conrad/sa/selfing/p7bowtie', 'min_mapq': '15', 'original_in_fhands': [<open file 'tcacao_lane6_11_GGCTAC.fastq', mode 'rt'>], 'out_fhand': <open file 'lane6_11.filtered.fastq', mode 'wt'>, 'out_format': 'fastq', 'paired_reads': True, 'processes': 1, ...} workers = None

/Library/Python/2.7/site-packages/crumbs/seqio.py in write_filter_packets(passed_fhand=<open file 'lane6_11.filtered.fastq', mode 'wt'>, filtered_fhand=<open file 'lane6_11.vectorhit.fastq', mode 'wt'>, filter_packets=, file_format='fastq', workers=None) 134 _write_filter_trim_packets(passed_fhand, filtered_fhand, filter_packets, 135 file_format=file_format, workers=workers, 136 seqs_diverted=SEQS_FILTERED_OUT) 137 138 seqs_diverted undefined global SEQS_FILTERED_OUT = 'seqs_filtered_out'

/Library/Python/2.7/site-packages/crumbs/seqio.py in _write_filter_trim_packets(passed_fhand=<open file 'lane6_11.filtered.fastq', mode 'wt'>, diverted_fhand=<open file 'lane6_11.vectorhit.fastq', mode 'wt'>, packets=, file_format='fastq', workers=None, seqs_diverted='seqs_filtered_out') 110 111 flatten_pairs = lambda pairs: (seq for pair in pairs for seq in pair) 112 for packet in packets: 113 try: 114 write_seqs(flatten_pairs(packet[SEQS_PASSED]), fhand=passed_fhand, packet undefined packets =

/Library/Python/2.7/site-packages/crumbs/utils/seq_utils.py in call(self=, seq_packet={'seqs_filtered_out': [], 'seqs_passed': [[SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...G3ID##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@17\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...BGCD<3\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDEB92\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@<:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...,@@@@#\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...>CACII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIIHII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...::::@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDD<GG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@7@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...8BDB2E\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...1@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EEGGG>\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...575517\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIBHBI\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EFEGCG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...CB3B##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...:::177\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EBF8DD\n'), annotations={}), file_format='fastq')], ...]}) 92 processed_packet = seq_packet 93 for map_function in self.map_functions: 94 processed_packet = map_function(processed_packet) 95 return processed_packet 96 processed_packet = {'seqs_filtered_out': [], 'seqs_passed': [[SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...G3ID##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@17\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...BGCD<3\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDEB92\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@<:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...,@@@@#\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...>CACII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIIHII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...::::@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDD<GG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@7@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...8BDB2E\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...1@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EEGGG>\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...575517\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIBHBI\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EFEGCG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...CB3B##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...:::177\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EBF8DD\n'), annotations={}), file_format='fastq')], ...]} map_function =

/Library/Python/2.7/site-packages/crumbs/filters.py in call(self=, filterpacket={'seqs_filtered_out': [], 'seqs_passed': [[SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...G3ID##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@17\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...BGCD<3\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDEB92\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@<:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...,@@@@#\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...>CACII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIIHII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...::::@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDD<GG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@7@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...8BDB2E\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...1@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EEGGG>\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...575517\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIBHBI\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EFEGCG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...CB3B##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...:::177\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EBF8DD\n'), annotations={}), file_format='fastq')], ...]}) 65 66 def call(self, filterpacket): 67 self._setup_checks(filterpacket) 68 reverse = self.reverse 69 failed_drags_pair = self.failed_drags_pair self = self._setup_checks = <bound method FilterBowtie2Match._setup_checks of > filterpacket = {'seqs_filtered_out': [], 'seqs_passed': [[SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...G3ID##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@17\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...BGCD<3\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDEB92\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@<:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...,@@@@#\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...>CACII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIIHII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...::::@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDD<GG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@7@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...8BDB2E\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...1@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EEGGG>\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...575517\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIBHBI\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EFEGCG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...CB3B##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...:::177\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EBF8DD\n'), annotations={}), file_format='fastq')], ...]}

/Library/Python/2.7/site-packages/crumbs/filters.py in _setup_checks(self=, filterpacket={'seqs_filtered_out': [], 'seqs_passed': [[SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...G3ID##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@17\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...BGCD<3\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDEB92\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@@<:\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...,@@@@#\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...>CACII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIIHII\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...::::@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EDD<GG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...@@@7@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...8BDB2E\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...1@@@@@\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EEGGG>\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...575517\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n"), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...HIBHBI\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EFEGCG\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...######\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...CB3B##\n'), annotations={}), file_format='fastq')], [SeqWrapper(kind='seqitem', object=SeqItem(name='...:::177\n'), annotations={}), file_format='fastq'), SeqWrapper(kind='seqitem', object=SeqItem(name='...EBF8DD\n'), annotations={}), file_format='fastq')], ...]}) 308 extra_params=extra_params) 309 310 self.mapped_reads = _get_mapped_reads(bam_fhand.name, self.min_mapq) 311 312 def _do_check(self, seq): self = self.mapped_reads undefined global _get_mapped_reads = bam_fhand = <open file '', mode 'w+b'> bam_fhand.name = '/var/folders/2s/v7ysbj65567frppd7chgrq700000gn/T/tmp5U21Pv.bam' self.min_mapq = '15'

/Library/Python/2.7/site-packages/crumbs/filters.py in _get_mapped_reads(bam_fpath='/var/folders/2s/v7ysbj65567frppd7chgrq700000gn/T/tmp5U21Pv.bam', min_mapq='15') 182 183 def _get_mapped_reads(bam_fpath, min_mapq=0): 184 bam = pysam.Samfile(bam_fpath) 185 return [read.qname for read in bam if not read.is_unmapped and (not min_mapq or read.mapq > min_mapq)] 186 bam undefined global pysam = <module 'pysam' from '/Library/Python/2.7/site-packages/pysam/init.pyc'> pysam.Samfile = <type 'pysam.csamtools.Samfile'> bam_fpath = '/var/folders/2s/v7ysbj65567frppd7chgrq700000gn/T/tmp5U21Pv.bam'

/Users/conrad/sa/selfing/analyses/tcacao_lane6_11_GGCTAC/ABySS/csamtools.pyx in pysam.csamtools.Samfile.cinit (pysam/csamtools.c:8722)()

/Users/conrad/sa/selfing/analyses/tcacao_lane6_11_GGCTAC/ABySS/csamtools.pyx in pysam.csamtools.Samfile._open (pysam/csamtools.c:9359)()

/Users/conrad/sa/selfing/analyses/tcacao_lane6_11_GGCTAC/ABySS/csamtools.pyx in pysam.csamtools.Samfile._open (pysam/csamtools.c:10460)()

<type 'exceptions.ValueError'>: file header is empty (mode='r') - is it SAM/BAM format? class = <type 'exceptions.ValueError'> delattr = <method-wrapper 'delattr' of exceptions.ValueError object> dict = {} doc = 'Inappropriate argument value (of correct type).' format = getattribute = <method-wrapper 'getattribute' of exceptions.ValueError object> getitem = <method-wrapper 'getitem' of exceptions.ValueError object> getslice = <method-wrapper 'getslice' of exceptions.ValueError object> hash = <method-wrapper 'hash' of exceptions.ValueError object> init = <method-wrapper 'init' of exceptions.ValueError object> new = reduce = reduce_ex = repr = <method-wrapper 'repr' of exceptions.ValueError object> setattr = <method-wrapper 'setattr' of exceptions.ValueError object> setstate = sizeof = str = <method-wrapper 'str' of exceptions.ValueError object> subclasshook = unicode = args = ("file header is empty (mode='r') - is it SAM/BAM format?",) message = "file header is empty (mode='r') - is it SAM/BAM format?"

The above is a description of an error in a Python program. Here is the original traceback:

Traceback (most recent call last): File "/Library/Python/2.7/site-packages/crumbs/utils/bin_utils.py", line 61, in main return(funct()) File "/Users/conrad/utils/bin/filter_by_bowtie2", line 79, in filter_by_bowtie2 args['out_format'], workers=workers) File "/Library/Python/2.7/site-packages/crumbs/seqio.py", line 136, in write_filter_packets seqs_diverted=SEQS_FILTERED_OUT) File "/Library/Python/2.7/site-packages/crumbs/seqio.py", line 112, in _write_filter_trim_packets for packet in packets: File "/Library/Python/2.7/site-packages/crumbs/utils/seq_utils.py", line 94, in call processed_packet = map_function(processed_packet) File "/Library/Python/2.7/site-packages/crumbs/filters.py", line 67, in call self._setup_checks(filterpacket) File "/Library/Python/2.7/site-packages/crumbs/filters.py", line 310, in _setup_checks self.mapped_reads = _get_mapped_reads(bam_fhand.name, self.min_mapq) File "/Library/Python/2.7/site-packages/crumbs/filters.py", line 184, in _get_mapped_reads bam = pysam.Samfile(bam_fpath) File "csamtools.pyx", line 736, in pysam.csamtools.Samfile.cinit (pysam/csamtools.c:8722) File "csamtools.pyx", line 781, in pysam.csamtools.Samfile._open (pysam/csamtools.c:9359) File "csamtools.pyx", line 891, in pysam.csamtools.Samfile._open (pysam/csamtools.c:10460) ValueError: file header is empty (mode='r') - is it SAM/BAM format?

The command was: /Users/conrad/utils/bin/filter_by_bowtie2 -t fastq -o lane6_11.filtered.fastq --paired_reads -i /Users/conrad/sa/selfing/p7bowtie -m 15 --fail_drags_pair True -e lane6_11.vectorhit.fastq tcacao_lane6_11_GGCTAC.fastq