MEGAN 6 Java IOException when opening .rma file

Bug Reports
1

I am currently using MEGAN6 Ultimate version 6.18.5 on MacOS (10.14.6 Mojave).

When I try to open .rma files with MEGAN (created with MALT) the following error occurs:

Executing: open file=’/Volumes/swarts/lab/Sonja/HB0293_GAACGCTG-AATACCGG_L001.rma’;
IOException: Bytes read: -1, expected: 1
Command usage: open file= [readOnly={false|true}]; - Open a MEGAN file (ending on .rma, .meg or .megan)
IOException: Bytes read: -1, expected: 1
Error: Execute failed: java.io.IOException: Bytes read: -1, expected: 1

This happens with several .rma files created within years (also different versions of MALT) independent from the storage location of the file.
Older versions of MEGAN can open part of them. Is this somehow correlating with versions of the input files?

Thanks,

Sonja

2

Dear Sonja,

please give me access to one of these files and I will look into this.

3

This is one example file. Thanks for your help.

https://drive.google.com/open?id=1RPj7OVpMs4cMvNcD24BEWC8j4L4kfqLY

Best,
Sonja

4

Dear Sonja,

I have taken a look at your file. It appears to have been generated by an old version of MALT and is in the old RMA3 format. This format isn’t used much any more and so a couple of bugs have crept into MEGAN over time. I have identified the bugs and will upload a release in which the bugs are fixed.
Before I create a new release, I just wanted to check with you:
The file contains nearly 700,000 reads, but none of the reads has any alignments. Does that sound right? If it is indeed the case that these reads did not align to anything, do you have an example file that definitely contains alignments? I would then check alignments are correctly read in and reported.
Daniel

5

I have built a new release and am now uploading it, V6_18_9