Could not open alignment file EXAMPLE-sorted.bam

[noisrevni]

When I ran the example after reinstalled PneumoCaT, it showed:

`(py2718) cyl@cyl-TravelMate-P249-MG:~/PneumoCaT/PneumoCaT-1.2.1$ python PneumoCaT.py -i /home/cyl/PneumoCaT/PneumoCaT_1.2.1/Examples/PHESPV0253 -o /home/cyl/batch1/serotype/Example
running bowtie index
[E::hts_open_format] Failed to open file "/home/cyl/batch1/serotype/Example/PHESPV0253-sorted.bam" : No such file or directory
There was an error in the function 'best_coverage'

---

Traceback (most recent call last):
File "/home/cyl/PneumoCaT/PneumoCaT_1.2.1/modules/utility_functions.py", line 59, in try_and_except
return function(*parameters, **named_parameters)
File "/home/cyl/PneumoCaT/PneumoCaT_1.2.1/modules/Serotype_determiner_functions.py", line 215, in best_coverage
bamfile = pysam.Samfile(bam, "rb")
File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open
IOError: [Errno 2] could not open alignment file /home/cyl/batch1/serotype/Example/PHESPV0253-sorted.bam: No such file or directory`