kskuchin
commented
3 years ago I had this same issue, as well as an error about an unexpected number of columns - both related to the core.import_starjxns() reading in of the junctions file.
I basically just cloned the repo, went into starseqr_utils/core.py and removed "header=None" in the pd.read_csv() call (line 31), and that seemed to fix it.
Dec 05 09:41:16 ..... loading genome Dec 05 09:42:08 ..... started mapping Dec 05 09:53:04 ..... finished mapping Dec 05 09:53:04 ..... finished successfully
2020-12-05 09:53 - INFO - STAR Alignment Finished! 2020-12-05 09:53 - INFO - Importing junctions 2020-12-05 09:54 - ERROR - There was a problem reading your STAR *Chimeric.out.junction file 2020-12-05 09:54 - ERROR - Exception: could not convert string to float: NreadsUnique 33113327 Traceback (most recent call last): File "/usr/bin/starseqr.py", line 622, in
sys.exit(main())
File "/usr/bin/starseqr.py", line 286, in main
rawdf = su.core.import_starjxns(new_prefix + ".Chimeric.out.junction", args.keep_dups, args.keep_mito)
File "/usr/lib64/python2.7/site-packages/starseqr_utils/core.py", line 55, in importstarjxns
raise(ValueError, e, traceback)
File "/usr/lib64/python2.7/site-packages/starseqr_utils/core.py", line 36, in import_starjxns
df['pos1'] = df['pos1'].astype(float).astype(int) # this bypasses some strange numbers
File "/usr/lib64/python2.7/site-packages/pandas/core/generic.py", line 5691, in astype
kwargs)
File "/usr/lib64/python2.7/site-packages/pandas/core/internals/managers.py", line 531, in astype
return self.apply('astype', dtype=dtype, kwargs)
File "/usr/lib64/python2.7/site-packages/pandas/core/internals/managers.py", line 395, in apply
applied = getattr(b, f)(kwargs)
File "/usr/lib64/python2.7/site-packages/pandas/core/internals/blocks.py", line 534, in astype
kwargs)
File "/usr/lib64/python2.7/site-packages/pandas/core/internals/blocks.py", line 633, in _astype
values = astype_nansafe(values.ravel(), dtype, copy=True)
File "/usr/lib64/python2.7/site-packages/pandas/core/dtypes/cast.py", line 702, in astype_nansafe
return arr.astype(dtype, copy=True)
ValueError: could not convert string to float: NreadsUnique 33113327