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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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Problem with running SAM format input #22

Closed vsbonthala closed 4 years ago

vsbonthala commented 4 years ago

Hi,

I am trying to run the working example on my machine (CentOS) following the instructions. However, I am getting error when try to feed syri with SAM format and the following commands were used: minimap2 -ax asm5 --eqx refgenome qrygenome > out.sam syri -c out.sam -r refgenome -q qrygenome -k -F S syri - WARNING - starting Reading Coords - ERROR - Error in reading the SAM file

However, when I use the nucmer, then I am getting results from syri without any issue. Please let me know why syri raises error when the input is in SAM format.

Thank you,

Best regards, Suresh

mnshgl0110 commented 4 years ago

Are you trying with python3.5? I think, using that would fix this problem. If not, then can you please share the log file after running syri with --log DEBUG parameter.

vsbonthala commented 4 years ago

I am using Python v3.7.3.

The log information as follows:

2020-01-10 09:10:48,449 - matplotlib - DEBUG - :1634 - matplotlib version 3.1.0 2020-01-10 09:10:48,449 - matplotlib - DEBUG - :1635 - interactive is False 2020-01-10 09:10:48,449 - matplotlib - DEBUG - :1636 - platform is linux 2020-01-10 09:10:48,450 - matplotlib - DEBUG - :1637 - loaded modules: ['sys', 'builtins', '_frozen_importlib', '_imp', '_thread', '_warnings', '_weakref', 'zipimport', '_frozen_importlib_external', '_io', 'marshal', 'posix', 'encodings', 'codecs', '_codecs', 'encodings.aliases', 'encodings.utf_8', '_signal', 'main', 'encodings.latin_1', 'io', 'abc', '_abc', 'site', 'os', 'stat', '_stat', 'posixpath', 'genericpath', 'os.path', '_collections_abc', '_sitebuiltins', '_bootlocale', '_locale', 'types', 'importlib', 'importlib._bootstrap', 'importlib._bootstrap_external', 'warnings', 'importlib.util', 'importlib.abc', 'importlib.machinery', 'contextlib', 'collections', 'operator', '_operator', 'keyword', 'heapq', '_heapq', 'itertools', 'reprlib', '_collections', 'functools', '_functools', 'mpl_toolkits', 'sphinxcontrib', 'argparse', 're', 'enum', 'sre_compile', '_sre', 'sre_parse', 'sre_constants', 'copyreg', 'gettext', 'locale', 'errno', 'logging', 'time', 'traceback', 'linecache', 'tokenize', 'token', 'weakref', '_weakrefset', 'collections.abc', 'string', '_string', 'threading', 'atexit', 'logging.config', 'logging.handlers', 'socket', '_socket', 'selectors', 'math', 'select', 'pickle', 'struct', '_struct', '_compat_pickle', '_pickle', 'queue', '_queue', 'socketserver', 'syri', 'syri.pyxFiles', 'syri.pyxFiles.synsearchFunctions', '_cython_0_29_12', 'cython_runtime', 'numpy', 'future', 'numpy._globals', 'numpy.config', 'numpy.version', 'numpy._distributor_init', 'ctypes', '_ctypes', 'ctypes._endian', 'numpy._mklinit', 'numpy.core', 'numpy.core.info', 'numpy.core.multiarray', 'numpy.core.overrides', 'datetime', '_datetime', 'numpy.core._multiarray_umath', 'numpy.compat', 'numpy.compat._inspect', 'numpy.compat.py3k', 'pathlib', 'fnmatch', 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'timeit', 'bottleneck.benchmark.bench_detailed', 'bottleneck.tests', 'bottleneck.tests.util', 'pandas.tseries', 'pandas.tseries.offsets', 'dateutil.easter', 'pandas.core.tools', 'pandas.core.tools.datetimes', 'pandas.core.sorting', 'pandas.core.arrays.datetimes', 'pandas.core.arrays.datetimelike', 'pandas.tseries.frequencies', 'pandas.core.arrays._ranges', 'pandas.core.arrays.interval', 'pandas.util._doctools', 'pandas.core.indexes', 'pandas.core.indexes.base', 'pandas._libs.index', 'pandas._libs.join', 'pandas.core.dtypes.concat', 'pandas.core.indexes.frozen', 'pandas.core.strings', 'pandas.core.arrays.period', 'pandas.core.arrays.timedeltas', 'pandas.core.arrays.integer', 'pandas.core.tools.numeric', 'pandas.core.arrays.sparse', 'pandas.libs.sparse', 'pandas.core.arrays.numpy', 'pandas.core.groupby', 'pandas.core.groupby.groupby', 'pandas._libs.groupby', 'pandas.core.frame', 'pandas.core.generic', 'json', 'json.decoder', 'json.scanner', '_json', 'json.encoder', 'pandas.core.index', 'pandas.core.indexes.api', 'pandas.core.indexes.category', 'pandas.core.indexes.datetimes', 'pandas.core.indexes.datetimelike', 'pandas.core.tools.timedeltas', 'pandas.core.indexes.numeric', 'pandas.core.indexes.interval', 'pandas.util._exceptions', 'pandas.core.indexes.multi', 'pandas.core.indexes.timedeltas', 'pandas.core.indexes.period', 'pandas.core.indexes.range', 'pandas.core.indexing', 'pandas._libs.indexing', 'pandas.core.internals', 'pandas.core.internals.blocks', 'pandas._libs.internals', 'pandas.core.internals.arrays', 'pandas.core.internals.managers', 'pandas.core.internals.concat', 'pandas.io.formats.format', 'pandas.io.common', 'csv', '_csv', 'mmap', 'zipfile', 'pandas.core.internals.construction', 'pandas.core.series', 'pandas.core.indexes.accessors', 'pandas.plotting', 'pandas.plotting._misc', 'pandas.plotting._style', 'pandas.plotting._tools', 'pandas.plotting._core', 'pandas.plotting._compat', 'pandas.plotting._converter', 'matplotlib', 'matplotlib.cbook', 'glob', 'matplotlib.cbook.deprecation', 'matplotlib.rcsetup', 'matplotlib.fontconfig_pattern', 'pyparsing', 'matplotlib.colors', 'matplotlib._color_data', 'cycler', 'matplotlib._version', 'kiwisolver'] 2020-01-10 09:10:48,963 - syri - WARNING - :115 - starting 2020-01-10 09:10:48,963 - syri - DEBUG - :115 - memory usage: 0.0828399658203125 2020-01-10 09:10:48,964 - Reading Coords - DEBUG - :115 - S 2020-01-10 09:10:48,964 - Reading Coords - INFO - :115 - Reading input from .tsv file 2020-01-10 09:10:48,964 - Reading Coords - ERROR - :115 - Error in reading the SAM file

mnshgl0110 commented 4 years ago

Please try running SyRI with python 3.5. Most probably that would resolve the issue.