MEGAN CE 6.25.10: Unreasonable string length

Bug Reports
1

Dear all,

Megan Community Edition 6.25.10
Ubuntu Server with kernel 5.15.0-122
File causing error: 50-2-05-2020.rma with ca. 13 GB

When trying to re-analyse an older rma file I get the following error, no matter if opened it in the GUI or with rma2info, for example:

rma2info -l -i 50-2-05-2020.rma

Version MEGAN Community Edition (version 6.25.10, built 27 Jun 2024)
Author(s) Daniel H. Huson
Copyright (C) 2024. This program comes with ABSOLUTELY NO WARRANTY.
Java version: 20.0.2; max memory: 125G
Caught:
java.io.IOException: Unreasonable string length: 1380794678
at megan/megan.io.InputOutputReaderWriter.readString(InputOutputReaderWriter.java:92)
at megan/megan.rma6.FooterSectionRMA6.read(FooterSectionRMA6.java:55)
at megan/megan.rma6.RMA6File.load(RMA6File.java:75)
at megan/megan.rma6.RMA6File.(RMA6File.java:62)
at megan/megan.rma6.RMA6Connector.getAuxiliaryData(RMA6Connector.java:212)
at megan/megan.core.SyncArchiveAndDataTable.syncArchive2Summary(SyncArchiveAndDataTable.java:72)
at megan/megan.core.Document.reloadFromConnector(Document.java:252)
at megan/megan.core.Document.loadMeganFile(Document.java:233)
at megan/megan.tools.RMA2Info.run(RMA2Info.java:118)
at megan/megan.tools.RMA2Info.main(RMA2Info.java:56)

This “problem file” is one of 144 which have been analysed multiple times without problems.
At first, I thought the file might be corrupt and rsynced it from another server (backup), which gave the same error.
I also tried with MEGAN CE 6.24.11 and 6.24.22 which are still installed on two other servers … same error.

I am now re-doing the diamond alignment and MEGAN annotation but am curious to know what is wrong with this particular file and how to interpret the error message.

Thanks,
Ralf

2

Hi @ralf_m,

Would it be possible for you to send this file so we can investigate it further? For future reference, it would be best to use the DAA format.

Best regards,
Anupam

3

Hi @Anupam,

Thanks for your reply!
Is there an option to upload the file (ca. 13 GB).

By the way, I used to use daa flies and daa-meganizer in the past until we had serious issues with it (see Meganizing stuck at Writing 80%). To push forward, we switched to rma files and daa2rma back then.

Cheers,
Ralf

4

Hi @ralf_m,

It’s not possible to upload it to the community page, but you can try uploading it to OneDrive or Dropbox and share the link with us, and we can download it from there. Alternatively, I can share a OneDrive link with you, and you can upload it directly.

This issue has been resolved. You can find more information here:-

I also recommend switching to MEGAN7, as MEGAN6 will no longer receive updates moving forward MEGAN7-download

Best regards,
Anupam

5

Hi @Anupam,

I uploaded the file to Sign in to your account
Please let me know when you downloaded the file so I can delete it.

Thanks for the heads-up on the MEGAN 7 beta version.

Cheers,
Ralf

6

Hi @ralf_m,

Thanks for the file. I discussed this with Prof. Huson, and we confirmed that the file is indeed broken, which is why MEGAN can’t process it. You mentioned that the file was created from a DAA file. If you could share the DAA file with us, we can check for any issues during the conversion to RMA.

You can delete the RMA file.

Best regards,
Anupam

7

Hi @Anupam,

I do not have the daa file anymore, sorry.
However, back then I could extract names and paths with rma2info.
I have not touched the rma file since, so I was puzzled that I could not extract information anymore.

Cheers,
Ralf

8

Hi @ralf_m,

I recommend running Diamond again; this might resolve the issue. Feel free to contact us if the problem persists.

best regards,
Anupam