Question: SNAP Aligner errors via MIMoDd

2.0 years ago by

shambyross • 10 wrote:

Hello everyone, can anyone help me to solve this problem:

Traceback (most recent call last): File "/Users/rossshamby/galaxy/tool-dependencies/python3/3.4/wolma/package_python_3_4_x_lean/83407422ec16/lib/python3.4/runpy.py", line 170, in _run_module_as_main "__main__", mod_spec) File "/Users/rossshamby/galaxy/tool-dependencies/python3/3.4/wolma/package_python_3_4_x_lean/83407422ec16/lib/python3.4/runpy.py", line 85, in _run_code exec(code, run_globals) File "/Users/rossshamby/galaxy/tool-dependencies/mimodd/0.1.7.3/wolma/mimodd/3accdbe6503b/MiModD_venv/lib/python3.4/site-packages/MiModD/__main__.py", line 417, in <module> parse() File "/Users/rossshamby/galaxy/tool-dependencies/mimodd/0.1.7.3/wolma/mimodd/3accdbe6503b/MiModD_venv/lib/python3.4/site-packages/MiModD/__main__.py", line 399, in parse result = funcs-1 File "/Users/rossshamby/galaxy/tool-dependencies/mimodd/0.1.7.3/wolma/mimodd/3accdbe6503b/MiModD_venv/lib/python3.4/site-packages/MiModD/snap.py", line 779, in make_snap_argdictlist job_arglist.append(snap_call_argcheck(FuncInfo(func=snap_call, innerscope = False), args)) File "/Users/rossshamby/galaxy/tool-dependencies/mimodd/0.1.7.3/wolma/mimodd/3accdbe6503b/MiModD_venv/lib/python3.4/site-packages/MiModD/decox.py", line 40, in wrappee ret = f(arg_dict) File "/Users/rossshamby/galaxy/tool-dependencies/mimodd/0.1.7.3/wolma/mimodd/3accdbe6503b/MiModD_venv/lib/python3.4/site-packages/MiModD/snap.py", line 608, in snap_call_argcheck args['inputfiles'][0]) MiModD.ArgumentValidationError: Multiple read groups declared in input file /Users/rossshamby/galaxy/database/files/000/dataset_75.dat. Such input is not currently supported.

I am following the instruction on MiModD website on how to do sequence alignment.

Thank you,

Ross

software error • 619 views

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modified 2.0 years ago • written 2.0 years ago by shambyross • 10

2.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use one read group per input dataset to avoid the problem.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k

2.0 years ago by

shambyross • 10

shambyross • 10 wrote:

Hi Jen, Never mind my previous post. I have used picard to give a header and I am aligning as we speak.

Thank you again,

Ross

ADD COMMENT • link written 2.0 years ago by shambyross • 10

Glad this was worked out! Jen

ADD REPLY • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k

2.0 years ago by

shambyross • 10

shambyross • 10 wrote:

Hi Jen,

I use only one group - in reaheader tool I assign value of 1 to the group ID and then I use SNAP align tool to perform alignment. Therefore, i am pretty sure I am using only one read group.

I have found the actual script for this. Too bad I am still in the precess of learning python and have no clue how to fix the problem :)

Any input would be valuable.

Thanks again,

validate input headers and

# make sure each job has its header as a Header instance in args['header']
header = {}
if args['iformat'] in ('sam', 'bam'):
    try:
        header = samheader.Header.fromfile(args['inputfiles'][0], args.get('iformat'))
    except RuntimeError:
        # this causes misleading errors with wrong iformat and
        # other general failures => improve !!
        pass
    if len(header.get('RG', [])) > 1:
        raise ArgumentValidationError(
            'Multiple read groups declared in input file {0}. Such input is not currently supported.',
            args['inputfiles'][0])
if args.get('header'):
    custom_header = args['header']
    if not isinstance (custom_header, samheader.Header):
        try:
            custom_header = samheader.Header.fromsam(custom_header)
        except RuntimeError:
            raise ArgumentValidationError(
                'Unable to get header information from custom header argument for file {0}.',
                args['inputfiles'][0])
    if len(custom_header['RG']) != 1:
        raise ArgumentValidationError(
            'The header specified by the custom header argument must contain exactly one read group; {0} found.',
            len(custom_header['RG']))
    args['header'] = header or samheader.Header()
    args['header'].merge_rg(custom_header, 'replace')
else:
    if not header:
        if args['iformat'] in ('sam', 'bam'):
            raise ArgumentValidationError(
                'Could not get header information from input file {0}.\nYou may want to provide a separate header through the custom header parameter.',
                args['inputfiles'][0])
        else:
            raise ArgumentValidationError(
                'Missing header information for input file {0}. {1} files require custom header information.',
                args['inputfiles'][0], args['iformat'])
    if len(header['RG']) == 0:
        raise ArgumentValidationError(
            'Could not find read group information in the header of the input file {0}.\nYou may want to provide a separate header through the custom header parameter.',
            args['inputfiles'][0])
    args['header'] = header

return args

ADD COMMENT • link written 2.0 years ago by shambyross • 10

MiModD has its own forum for asking questions like this. You can also post there via email to mimodd@googlegroups.com. In general, this should be the place to turn to if you suspect something is wrong with MiModD itself, while this forum here is for asking questions about Galaxy. As another note, starting to dive into the internals of the package (or any software) should always be the very last thing to do. It is far more likely that there is a problem with the input rather than with the code and, as a beginner, you are also not very likely to improve things by manipulating source code. As a start you could have looked at a report of the read groups in your input data using the MiModD info tool, which serves exactly that purpose.

ADD REPLY • link written 2.0 years ago by Wolfgang Maier • 600

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validate input headers and

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