/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/xphyle-4.2.2-py3.6.egg/xphyle/paths.py:149: DeprecationWarning: Use of resolve_path with string path arguments is deprected (lineno /hpc/local/CentOS7/common/lang/python/3.6.1/lib/python3.6/argparse.py:2261)
  f"Use of {func.__name__} with string path arguments is "
2020-04-21 16:31:22.147 | INFO     | atropos.commands.console:_setup_logging:247 - This is Atropos 2.0.0-alpha.5-PMC with Python 3.6.1
%(asctime)s %(levelname)s: %(message)s
2020-04-21 16:31:22.209 | INFO     | atropos.commands.trim:__call__:625 - Trimming 1 adapter with at most 10.0 errors in single-end mode...
%(asctime)s %(levelname)s: %(message)s
2020-04-21 16:31:22.230 | ERROR    | atropos.utils:run_interruptible:154 - Atropos error
Traceback (most recent call last):

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 455, in handle_records
    self.handle_record(context, record)
    |    |             |        -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAACT...
    |    |             -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    -> <function SingleEndPipelineMixin.handle_record at 0x2b21d287a6a8>
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 508, in handle_record
    cast(Pipeline, self).handle_reads(context, record)
    |    |         |                  |        -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAACT...
    |    |         |                  -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    |         -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>
    |    -> <class 'atropos.commands.Pipeline'>
    -> <function cast at 0x2b21d07362f0>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/pipeline.py", line 192, in handle_reads
    return self.record_handler.handle_record(context, read1, read2)
           |    |              |             |        |      -> None
           |    |              |             |        -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAACT...
           |    |              |             -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
           |    |              -> <function RecordHandler.handle_record at 0x2b21d2ba77b8>
           |    -> <atropos.commands.trim.pipeline.RecordHandler object at 0x2b21d74ddf98>
           -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/pipeline.py", line 44, in handle_record
    self.formatters.format(context["results"], dest, *reads)
    |    |          |      |                   |      -> (<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCC', qualities='A6AAA...
    |    |          |      |                   -> <class 'atropos.commands.trim.filters.NoFilter'>
    |    |          |      -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    |          -> <function Formatters.format at 0x2b21d2ba7268>
    |    -> <atropos.commands.trim.writers.Formatters object at 0x2b21d74ddcf8>
    -> <atropos.commands.trim.pipeline.RecordHandler object at 0x2b21d74ddf98>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/writers.py", line 270, in format
    self.seq_formatters[dest].format(result, read1, read2)
    |    |              |            |       |      -> None
    |    |              |            |       -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCC', qualities='A6AAAE...
    |    |              |            -> {}
    |    |              -> <class 'atropos.commands.trim.filters.NoFilter'>
    |    -> {<class 'atropos.commands.trim.filters.NoFilter'>: <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>}
    -> <atropos.commands.trim.writers.Formatters object at 0x2b21d74ddcf8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 189, in format
    result_list = self._get_result_list(result, self._file1)
                  |    |                |       |    -> PosixPath('/home/gen/philip/tmp/atropos-testdata/TM433_trimmed2.sam')
                  |    |                |       -> <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>
                  |    |                -> {}
                  |    -> <function Formatter._get_result_list at 0x2b21d28ea1e0>
                  -> <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 143, in _get_result_list
    header = self._get_header()
             |    -> <function SAMFormatterMixin._get_header at 0x2b21d28ead90>
             -> <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 269, in _get_header
    rows.extend(create_row(tags) for tags in tags_list)
    |    |      |                            -> ['user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --t...
    |    |      -> <function SAMFormatterMixin._get_header.<locals>.create_row at 0x2b21d2c63488>
    |    -> <method 'extend' of 'list' objects>
    -> ['@HD\tVN:1.4', '@SQ\tSN:chr1\tLN:248956422', '@SQ\tSN:chr2\tLN:242193529', '@SQ\tSN:chr3\tLN:198295559', '@SQ\tSN:chr4\tLN:1...

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 269, in <genexpr>
    rows.extend(create_row(tags) for tags in tags_list)
                |          |         -> 'user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --tw...
                |          -> 'user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --tw...
                -> <function SAMFormatterMixin._get_header.<locals>.create_row at 0x2b21d2c63488>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 260, in create_row
    tags_str = "\t".join(f"{key}:{val}" for key, val in _tags.items())
                                                        -> 'user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --tw...

AttributeError: 'str' object has no attribute 'items'


The above exception was the direct cause of the following exception:


Traceback (most recent call last):
  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/bin/atropos", line 11, in <module>
    load_entry_point('atropos===2.0.0-alpha.5-PMC', 'console_scripts', 'atropos')()
    -> <function load_entry_point at 0x2b21d0696268>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/__main__.py", line 17, in main
    sys.exit(run_atropos(args))
    |   |    |           -> None
    |   |    -> <function run_atropos at 0x2b21cbb63268>
    |   -> <built-in function exit>
    -> <module 'sys' (built-in)>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/console.py", line 56, in run_atropos
    return execute_cli(args)
           |           -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '--input-format', 'bam', '-se', 'TM433_trunc.bam', '--output-format', 'sam', '-o', '...
           -> <function execute_cli at 0x2b21d2884840>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/console.py", line 144, in execute_cli
    retcode, summary = command.execute(args)
                       |       |       -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '--input-format', 'bam', '-se', 'TM433_trunc.bam', '--output-format', 'sam', '-o', '...
                       |       -> <classmethod object at 0x2b21d287f908>
                       -> atropos.commands.trim.console.TrimCommandConsole

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/console.py", line 144, in execute
    retcode, summary = command.run()
                       |       -> <function BaseCommand.run at 0x2b21d2875b70>
                       -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 324, in run
    self.return_code = self()
    |    |             -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>
    |    -> None
    -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/__init__.py", line 649, in __call__
    writers,
    -> <atropos.commands.trim.writers.Writers object at 0x2b21d74ddf60>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/serial.py", line 45, in run_serial
    raise_on_error=True

> File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/utils/__init__.py", line 144, in run_interruptible
    func(*args, **kwargs)
    |     |       -> {'raise_on_error': True}
    |     -> (<atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>,)
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 402, in __call__
    self.process_batch(batch)
    |    |             -> ({'index': 1, 'source': 0, 'size': 20}, [<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', ...
    |    -> <function Pipeline.process_batch at 0x2b21d287a1e0>
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 435, in process_batch
    self.handle_records(context, records)
    |    |              |        -> [<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAAC...
    |    |              -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    -> <function TrimPipeline.handle_records at 0x2b21d2bad9d8>
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/pipeline.py", line 186, in handle_records
    super().handle_records(context, records)
                           |        -> [<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAAC...
                           -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 459, in handle_records
    ) from err

atropos.errors.AtroposError: An error occurred at record 0 of batch 1
%(asctime)s %(levelname)s: %(message)s
Traceback (most recent call last):

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 455, in handle_records
    self.handle_record(context, record)
    |    |             |        -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAACT...
    |    |             -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    -> <function SingleEndPipelineMixin.handle_record at 0x2b21d287a6a8>
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 508, in handle_record
    cast(Pipeline, self).handle_reads(context, record)
    |    |         |                  |        -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAACT...
    |    |         |                  -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    |         -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>
    |    -> <class 'atropos.commands.Pipeline'>
    -> <function cast at 0x2b21d07362f0>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/pipeline.py", line 192, in handle_reads
    return self.record_handler.handle_record(context, read1, read2)
           |    |              |             |        |      -> None
           |    |              |             |        -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAACT...
           |    |              |             -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
           |    |              -> <function RecordHandler.handle_record at 0x2b21d2ba77b8>
           |    -> <atropos.commands.trim.pipeline.RecordHandler object at 0x2b21d74ddf98>
           -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/pipeline.py", line 44, in handle_record
    self.formatters.format(context["results"], dest, *reads)
    |    |          |      |                   |      -> (<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCC', qualities='A6AAA...
    |    |          |      |                   -> <class 'atropos.commands.trim.filters.NoFilter'>
    |    |          |      -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    |          -> <function Formatters.format at 0x2b21d2ba7268>
    |    -> <atropos.commands.trim.writers.Formatters object at 0x2b21d74ddcf8>
    -> <atropos.commands.trim.pipeline.RecordHandler object at 0x2b21d74ddf98>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/writers.py", line 270, in format
    self.seq_formatters[dest].format(result, read1, read2)
    |    |              |            |       |      -> None
    |    |              |            |       -> <Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCC', qualities='A6AAAE...
    |    |              |            -> {}
    |    |              -> <class 'atropos.commands.trim.filters.NoFilter'>
    |    -> {<class 'atropos.commands.trim.filters.NoFilter'>: <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>}
    -> <atropos.commands.trim.writers.Formatters object at 0x2b21d74ddcf8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 189, in format
    result_list = self._get_result_list(result, self._file1)
                  |    |                |       |    -> PosixPath('/home/gen/philip/tmp/atropos-testdata/TM433_trimmed2.sam')
                  |    |                |       -> <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>
                  |    |                -> {}
                  |    -> <function Formatter._get_result_list at 0x2b21d28ea1e0>
                  -> <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 143, in _get_result_list
    header = self._get_header()
             |    -> <function SAMFormatterMixin._get_header at 0x2b21d28ead90>
             -> <atropos.io.formatters.SingleEndSAMFormatter object at 0x2b21d74ddeb8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 269, in _get_header
    rows.extend(create_row(tags) for tags in tags_list)
    |    |      |                            -> ['user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --t...
    |    |      -> <function SAMFormatterMixin._get_header.<locals>.create_row at 0x2b21d2c63488>
    |    -> <method 'extend' of 'list' objects>
    -> ['@HD\tVN:1.4', '@SQ\tSN:chr1\tLN:248956422', '@SQ\tSN:chr2\tLN:242193529', '@SQ\tSN:chr3\tLN:198295559', '@SQ\tSN:chr4\tLN:1...

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 269, in <genexpr>
    rows.extend(create_row(tags) for tags in tags_list)
                |          |         -> 'user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --tw...
                |          -> 'user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --tw...
                -> <function SAMFormatterMixin._get_header.<locals>.create_row at 0x2b21d2c63488>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/io/formatters.py", line 260, in create_row
    tags_str = "\t".join(f"{key}:{val}" for key, val in _tags.items())
                                                        -> 'user command line: STAR --genomeDir /hpc/local/CentOS7/gen/data/genomes/human/gencode/STARindex_PARmask --runThreadN 16 --tw...

AttributeError: 'str' object has no attribute 'items'


The above exception was the direct cause of the following exception:


Traceback (most recent call last):
  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/bin/atropos", line 11, in <module>
    load_entry_point('atropos===2.0.0-alpha.5-PMC', 'console_scripts', 'atropos')()
    -> <function load_entry_point at 0x2b21d0696268>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/__main__.py", line 17, in main
    sys.exit(run_atropos(args))
    |   |    |           -> None
    |   |    -> <function run_atropos at 0x2b21cbb63268>
    |   -> <built-in function exit>
    -> <module 'sys' (built-in)>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/console.py", line 56, in run_atropos
    return execute_cli(args)
           |           -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '--input-format', 'bam', '-se', 'TM433_trunc.bam', '--output-format', 'sam', '-o', '...
           -> <function execute_cli at 0x2b21d2884840>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/console.py", line 144, in execute_cli
    retcode, summary = command.execute(args)
                       |       |       -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '--input-format', 'bam', '-se', 'TM433_trunc.bam', '--output-format', 'sam', '-o', '...
                       |       -> <classmethod object at 0x2b21d287f908>
                       -> atropos.commands.trim.console.TrimCommandConsole

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/console.py", line 144, in execute
    retcode, summary = command.run()
                       |       -> <function BaseCommand.run at 0x2b21d2875b70>
                       -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 324, in run
    self.return_code = self()
    |    |             -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>
    |    -> None
    -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/__init__.py", line 649, in __call__
    writers,
    -> <atropos.commands.trim.writers.Writers object at 0x2b21d74ddf60>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/serial.py", line 45, in run_serial
    raise_on_error=True

> File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/utils/__init__.py", line 144, in run_interruptible
    func(*args, **kwargs)
    |     |       -> {'raise_on_error': True}
    |     -> (<atropos.commands.trim.console.TrimCommandConsole object at 0x2b21d2be0f28>,)
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 402, in __call__
    self.process_batch(batch)
    |    |             -> ({'index': 1, 'source': 0, 'size': 20}, [<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', ...
    |    -> <function Pipeline.process_batch at 0x2b21d287a1e0>
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 435, in process_batch
    self.handle_records(context, records)
    |    |              |        -> [<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAAC...
    |    |              -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}
    |    -> <function TrimPipeline.handle_records at 0x2b21d2bad9d8>
    -> <atropos.commands.trim.serial.SingleEndSerialTrimPipeline object at 0x2b21d74ea048>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/trim/pipeline.py", line 186, in handle_records
    super().handle_records(context, records)
                           |        -> [<Sequence(name='NB500901:233:HJGGKBGXF:1:12108:16268:8303:cbc=AGCGATGG:umi=GGCAAG', sequence='TCGCTCTTGCCGATCGTCGGACTGTAGAAC...
                           -> {'index': 1, 'source': 0, 'size': 20, 'bp': [64, 0], 'results': {}}

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5-PMC/lib/python3.6/site-packages/atropos-2.0.0_alpha.5_PMC-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 459, in handle_records
    ) from err

atropos.errors.AtroposError: An error occurred at record 0 of batch 1
2020-04-21 16:31:22.260 | DEBUG    | atropos.commands.console:execute:149 - Not generating report file