PositionalAssembler Error

[DarioS]

I have processed six TCGA patients seemingly successfully, but there's one which ran until the allotted time and didn't complete. In the comprehensive log, I notice

WARNING	2019-10-05 02:23:34	PositionalAssembler	Error during assembly of chromosome GL000216.1 (3080 reads in graph). Attempting recovery by rebuilding assembly graph.
java.lang.IllegalArgumentException: support and aes sizes do not match
	at au.edu.wehi.idsv.AssemblyAttributes.annotateAssembly(AssemblyAttributes.java:146)
	at au.edu.wehi.idsv.AssemblyFactory.createAssemblySAMRecord(AssemblyFactory.java:202)
	at au.edu.wehi.idsv.AssemblyFactory.createAnchoredBreakend(AssemblyFactory.java:41)

The log file is many times larger than the same type of file for the other patients and this error appears multiple times in the log file, about 1 minute apart. How can I resolve the mismatch of "support" and "aes"? Should I try making a minimal example to trigger this issue?

[d-cameron]

Gridss 2.6.2 or 2.6.1?

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On Wed., 9 Oct. 2019, 12:08 pm Dario Strbenac, ***@***.***> wrote: — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#260?email_source=notifications&email_token=ABOBYOHAVJLYN2ENVKLOBCLQNUVI7A5CNFSM4I6Y24HKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HQP2RUA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABOBYOFHS4YCLGYI6U3RRPTQNUVI7ANCNFSM4I6Y24HA> .

[DarioS]

It's version 2.6.1 I don't notice anything in the change log for version 2.6.2 that would seem to make a difference.

[d-cameron]

There is assembly recovery logic in there. If assembly dies for any reason, 2.6.2 will do a clean reload of the reads in the assembly graph so either the edge case error will be avoided, or at least there will be a minimal set of reads to reproduce the error (the lingering issues have been because every time I try to reproduce locally, it works fine).

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On Wed., 9 Oct. 2019, 5:00 pm Dario Strbenac, ***@***.***> wrote: It's version 2.6.1 I don't notice anything in the change log for version 2.6.2 that would seem to make a difference. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#260?email_source=notifications&email_token=ABOBYOD6P54ZYBWWMAHBIKDQNVXORA5CNFSM4I6Y24HKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAWWUBQ#issuecomment-539847174>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABOBYOFIT4VSGGLNYRLJW5TQNVXORANCNFSM4I6Y24HA> .

[DarioS]

The error recurs in version 2.6.2 Which file has the minimal set of reads which I should share?

[d-cameron]

Give me a few days and I'll add code to automatically package up the minimal set of information required to reproduce any assembly error. Being able to ask for _gridss_error_minimal_reproduction_data_.zip to be uploaded with the issue should make finally fixing these remaining edge case bugs much much more straight-forward.

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On Sat, Oct 12, 2019 at 11:00 AM Dario Strbenac ***@***.***> wrote: The error recurs in version 2.6.2 Which file has the minimal set of reads which I should share? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#260?email_source=notifications&email_token=ABOBYODAD22HFQZ2RPTBBJLQOEHQNA5CNFSM4I6Y24HKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBBPQDA#issuecomment-541259788>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABOBYOFNB5JVEKMT2SZDE5DQOEHQNANCNFSM4I6Y24HA> .

[DarioS]

The problem seems fixed in version 2.6.3 of GRIDSS.

Wed Oct 23 05:27:54 AEDT 2019   Run complete with 19 warnings and 0 errors.