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husonlab / malt

MEGAN alignment tool
GNU General Public License v3.0
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Invalid, unknown or duplicate option: --format or -f #4

Open jfy133 opened 4 years ago

jfy133 commented 4 years ago

When running MALT version 0.4.1 (built 24 May 2018), and I try to export the alignments in SAM format, I get the following error when using either --format or -f

jloda.util.UsageException: Invalid, unknown or duplicate option: --format
, use option '-h' for help
        at jloda.util.ArgsOptions.done(ArgsOptions.java:210)
        at malt.MaltRun.run(MaltRun.java:215)
        at malt.MaltRun.main(MaltRun.java:75)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:65)
        at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

Example command:

malt-run -J-Xmx32g -t 8 -v -o . -d mini-database/ -id 85 -m BlastN -at SemiGlobal -top 1 -supp 0.01 -mq 100 --memoryMode load -i fastqs/* -ssc -sps --format