Question: SNAP Aligner errors via MIMoDd
0
gravatar for shambyross
21 months ago by
shambyross10
shambyross10 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 • 504 views
ADD COMMENTlink modified 21 months ago • written 21 months ago by shambyross10
1
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
1
gravatar for shambyross
21 months ago by
shambyross10
shambyross10 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 COMMENTlink written 21 months ago by shambyross10

Glad this was worked out! Jen

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson25k
0
gravatar for shambyross
21 months ago by
shambyross10
shambyross10 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 COMMENTlink written 21 months ago by shambyross10
1

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 REPLYlink written 21 months ago by Wolfgang Maier550
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