Filter_by_bowtie2

[ConradStack]

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=<itertools.imap object>, 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=<itertools.imap object>, 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 = <itertools.imap object>

/Library/Python/2.7/site-packages/crumbs/utils/seq_utils.py in call(self=<crumbs.utils.seq_utils._FunctionRunner object>, 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 = <crumbs.filters.FilterBowtie2Match object>

/Library/Python/2.7/site-packages/crumbs/filters.py in call(self=<crumbs.filters.FilterBowtie2Match object>, 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 = <crumbs.filters.FilterBowtie2Match object>
self._setup_checks = <bound method FilterBowtie2Match._setup_checks of <crumbs.filters.FilterBowtie2Match object>>
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=<crumbs.filters.FilterBowtie2Match object>, 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 = <crumbs.filters.FilterBowtie2Match object>
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