Error : 'i is not a recognized option'

[Lucas SENINGE]

Hello,

I am still a student and I have to deal with telomere length analysis in a project. I tried installing and running qmotif-1.2, since I've seen that it is one of the most efficient tool for measuring telomere length from WGS data. However, while running a test with a test bam file, I received the following error:

"qmotif: joptsimple.UnrecognizedOptionException: 'i' is not a recognized option
joptsimple.UnrecognizedOptionException: 'i' is not a recognized option
at joptsimple.OptionException.unrecognizedOption(OptionException.java:89)
at joptsimple.OptionParser.validateOptionCharacters(OptionParser.java:536)
at joptsimple.OptionParser.handleShortOptionCluster(OptionParser.java:447)
at joptsimple.OptionParser.handleShortOptionToken(OptionParser.java:442)
at joptsimple.OptionParserState$2.handleArgument(OptionParserState.java:59)
at joptsimple.OptionParser.parse(OptionParser.java:361)
at org.qcmg.motif.Options.<init>(Options.java:75)
at org.qcmg.motif.Motif.main(Motif.java:339)"

I think it comes from the line "-i /mydata/qmotif.ini \" ; the qmotif.ini is present in my file, so I don't know why the -i command is not recognized.
Any clue where it can come from? I am new to bioinformatics and don't have good knowledge of computer; maybe the solution is obvious but I am willing to learn and get better. If you can help me, I'll be grateful !
Best
Lucas

[Ollie Holmes]

Hi Lucas,
It looks like tthe problem is to do with your command line. Could you please check that all of the options that you supply are correct (ie. that they have a dash before them, a space after them and that any files they are referring to are present)?
If you are still experiencing the issue, please could you send me your entire command line?
Many thanks,
Ollie

[shihucai]

making --ini substitute for -i , it works.