How to use PhageTerm?

Question

[marongiu.luigi]

I am trying to use PhageTerm to analyze the genome of a hypothetical phage. I used:

$ python3 ~/src/phageterm/PhageTerm.py -f ~/Downloads/phage/pair_1.fq -p ~/Downloads/phage/pair_2.fq -r ~/Downloads/phage/ref.fa -c C5
Usage: 

Usage: PhageTerm.py -f reads.fastq -r phage_sequence.fasta [--report_title analysis_name -p reads_paired -s seed_lenght -d surrounding -t installation_test -c nbr_core -g host.fasta (warning increase process time) -l limit_multi-fasta -v virome_time]
[--mm --dir_cov_mm path_to_coverage_results -c nb_cores --core_id idx_core -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]
[--mm --dir_cov_mm path_to_coverage_results --dir_seq_mm path_to_sequence_results --DR_path path_to_results --seq_id index_of_sequence --nb_pieces nbr_of_read_chunks -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]
[--mm --DR_path path_to_results --dir_seq_mm path_to_sequence_results -p reads_paired -s seed_lenght -d surrounding -l limit_multi-fasta]

    Program: PhageTerm - Analyze phage termini and packaging mode using reads from high-throughput sequenced phage data
    Version: 3.0.1
    Contact: Julian Garneau <[e-mail]>
    Contact: David Bikard <[e-mail]>
    Contact: Marc Monot <[e-mail]>
    Contact: Veronique Legrand <[e-mail]>

    You can perform a program test run upon installation using the "-t " option.
    Arguments for the -t option can be : C5, C3, DS, DL, M , H or V

    Example of test commands :
    PhageTerm.py.py -t C5       -> Test run for a 5' cohesive end (e.g. Lambda)
    PhageTerm.py.py -t C3       -> Test run for a 3' cohesive end (e.g. HK97)
    PhageTerm.py.py -t DS     -> Test run for a Direct Terminal Repeats end short (e.g. T7)
    PhageTerm.py.py -t DL     -> Test run for a Direct Terminal Repeats end long (e.g. T5)
    PhageTerm.py.py -t H       -> Test run for a Headful packaging (e.g. P1)
    PhageTerm.py.py -t M       -> Test run for a Mu-like packaging (e.g. Mu)
    PhageTerm.py.py -t V       -> Test run for a Virome data


PhageTerm.py: error: option -c: invalid integer value: 'C5'

$ python3 ~/src/phageterm/PhageTerm.py -f ~/Downloads/phage/pair_1.fq -p ~/Downloads/phage/pair_2.fq -r ~/Downloads/phage/ref.fa -t C5

Performing a test run using test phage sequence with 5 prime cohesive overhang :

python PhageTerm.py -f test-data/COS-5.fastq -r test-data/COS-5.fasta -n TEST_cohesive_5_prime
Traceback (most recent call last):
  File "/home/gigiux/src/phageterm/PhageTerm.py", line 327, in <module>
    main()
  File "/home/gigiux/src/phageterm/PhageTerm.py", line 58, in main
    inRawDArgs, fParms, tParms, inDArgs=checkOptArgsConsistency(getopt)
  File "/home/gigiux/src/phageterm/_modules/main_utils.py", line 481, in checkOptArgsConsistency
    inRawDArgs = inputRawDataArgs(options.fastq, options.reference, options.host, options.analysis_name, options.paired,
  File "/home/gigiux/src/phageterm/_modules/main_utils.py", line 223, in __init__
    if checkFastaFile(reference):
  File "/home/gigiux/src/phageterm/_modules/main_utils.py", line 50, in checkFastaFile
    infil = open(filin, 'r')
FileNotFoundError: [Errno 2] No such file or directory: 'test-data/COS-5.fasta'

I am using uncompressed fastq files.

What is the correct use?