the problem of -u(--abnormalUnmapFlag from wrapper)

[snowylxx]

So I run the TRUST4, here was a error that cause there were not outfiles.
error: Two reads from the unaligned fragment are not showing up together. Please use -u(--abnormalUnmapFlag from wrapper) option.
I see the bam file is pair-end. how to handle this?

[Li Song]

You just need to add the "--abnormalUnmapFlag" option when using the "run-trust4" command.

[snowylxx]

oh ,thanks!

[snowylxx]

so I add the option but there were another error occurred:
/software/TRUST4-1.0.12/bam-extractor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /software/TRUST4-1.0.12/bam-extractor: /software/TRUST4-1.0.12/bam-extractor) /software/TRUST4-1.0.12/bam-extractor: /lib64/libstdc++.so.6: version CXXABI_1.3.8' not found (required by /software/TRUST4-1.0.12/bam-extractor)
/software/TRUST4-1.0.12/bam-extractor: /lib64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by /software/TRUST4-1.0.12/bam-extractor) /software/TRUST4-1.0.12/bam-extractor: /lib64/libstdc++.so.6: version GLIBCXX_3.4.29' not found (required by /software/TRUST4-1.0.12/bam-extractor)
/software/TRUST4-1.0.12/bam-extractor: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /software/TRUST4-1.0.12/bam-extractor)

[Li Song]

How did you install TRUST4?
This is strange. You should receive this error in your first run. Adding the "--abnormalUnmapFlag" should not create libstdc++ issue.

[snowylxx]

I just need to log out and rerun the program again.

But I have one more question. I will run multiple bam files at once, and some will prompt: Two reads from the unaligned fragment are not showing up together Please use - u (-- abnormalUnmapFlag from wrapper) option. Some can be run directly. May I add the option '-- abnormalUnmapFlag' for all files for convenience?

[Li Song]

Yes, you may add the option for all files. It should not affect the results.

[snowylxx]

thanks a lot for your help. The program ran very smoothly.