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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
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.fq.gz files not accepted for input #30

Open TimHHH opened 4 years ago

TimHHH commented 4 years ago

.fq.gz files are not accepted for input, they result in this error:

Traceback (most recent call last):
  File "/home/shared_data_ghi/CWGSMTB/Software/venv_resetqtb-uvp/bin/uvp", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/home/shared_data_ghi/CWGSMTB/Software/resetqtb-uvp/bin/uvp", line 181, in <module>
    main()
  File "/home/shared_data_ghi/CWGSMTB/Software/resetqtb-uvp/bin/uvp", line 158, in main
    s.runFastQC()
  File "/home/shared_data_ghi/CWGSMTB/Software/resetqtb-uvp/uvp/snp.py", line 185, in runFastQC
    fh1 = open(fastqcOut, 'r')
FileNotFoundError: [Errno 2] No such file or directory: 'Results/./test01/fastqc/NC-000962-3-H37Rv_mutated_1.30.1.fq.gz/summary.txt'

changing the file extension to fastq.gz fixes the issue

Tim