Error when loading meganized files

Bug Reports
1

Hi, I just got a new computer (running Windows 11, 32GB RAM). I just downloaded the latest version of MEGAN6 (MEGAN_Community_windows-x64_6_24_20.exe). I have used MEGAN in the past to meganize and analyze daa files on my old machine. But now when I try to open those same files I get the following error:

Executing: add file=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Raj’s Erie Coke Analysis\DIAMOND-MEGAN Files\Meganized DAA Files\Diamond_ESO1A__DAA_output__forward.daa’;
IOExceptionWithLineNumber: Line 1: ‘;’ expected, got: ‘s’
Command usage: add file=; - Add files for comparison
IOException: Line 1: ‘;’ expected, got: ‘s’
Error: Execute failed: java.io.IOException: Line 1: ‘;’ expected, got: ‘s’
Executing: cancel;
Selected: 0
Executing: open file=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Raj’s Erie Coke Analysis\DIAMOND-MEGAN Files\Meganized DAA Files\Diamond_ESO1A__DAA_output__forward.daa’;
IOExceptionWithLineNumber: Line 1: ‘;’ expected, got: ‘s’
Command usage: open file= [readOnly={false|true}]; - Open a MEGAN file (ending on .rma, .meg or .megan)
IOException: Line 1: ‘;’ expected, got: ‘s’
Error: Execute failed: java.io.IOException: Line 1: ‘;’ expected, got: ‘s’

I have also tried to meganize new daa files and I get the following error when I load the Meganmapdb file (megan-map-Feb2022.db):

Executing: show window=MeganizeDAA;
Loading ec.map: 8,200
Loading ec.tre: 8,204
Loading eggnog.map: 30,875
Loading eggnog.tre: 30,986
Loading gtdb.map: 240,103
Loading gtdb.tre: 240,107
Loading interpro2go.map: 14,242
Loading interpro2go.tre: 28,907
Loading seed.map: 961
Loading seed.tre: 962
Executing: use cViewer=CARD state=false;
Executing: load mapFile=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Colleen’s Forensics Analysis\megan-map-Feb2022.db’ mapType=MeganMapDB cName=EC;
IOExceptionWithLineNumber: Line 1: ‘mapType’ expected, got: ‘s’
Command usage: load mapFile= mapType=<Accession|Synonyms|MeganMapDB> cName=<CARD|EC|EGGNOG|GTDB|INTERPRO2GO|KEGG|PGPT|SEED|Taxonomy> [parseTaxonNames={false|true}]; - Loads a mapping file
Error: Command failed: Line 1: ‘mapType’ expected, got: ‘s’
Executing: use cViewer=EC state=true;
Executing: load mapFile=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Colleen’s Forensics Analysis\megan-map-Feb2022.db’ mapType=MeganMapDB cName=EGGNOG;
IOExceptionWithLineNumber: Line 1: ‘mapType’ expected, got: ‘s’
Command usage: load mapFile= mapType=<Accession|Synonyms|MeganMapDB> cName=<CARD|EC|EGGNOG|GTDB|INTERPRO2GO|KEGG|PGPT|SEED|Taxonomy> [parseTaxonNames={false|true}]; - Loads a mapping file
Error: Command failed: Line 1: ‘mapType’ expected, got: ‘s’
Executing: use cViewer=EGGNOG state=true;
Executing: load mapFile=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Colleen’s Forensics Analysis\megan-map-Feb2022.db’ mapType=MeganMapDB cName=GTDB;
IOExceptionWithLineNumber: Line 1: ‘mapType’ expected, got: ‘s’
Command usage: load mapFile= mapType=<Accession|Synonyms|MeganMapDB> cName=<CARD|EC|EGGNOG|GTDB|INTERPRO2GO|KEGG|PGPT|SEED|Taxonomy> [parseTaxonNames={false|true}]; - Loads a mapping file
Error: Command failed: Line 1: ‘mapType’ expected, got: ‘s’
Executing: use cViewer=GTDB state=true;
Executing: load mapFile=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Colleen’s Forensics Analysis\megan-map-Feb2022.db’ mapType=MeganMapDB cName=INTERPRO2GO;
IOExceptionWithLineNumber: Line 1: ‘mapType’ expected, got: ‘s’
Command usage: load mapFile= mapType=<Accession|Synonyms|MeganMapDB> cName=<CARD|EC|EGGNOG|GTDB|INTERPRO2GO|KEGG|PGPT|SEED|Taxonomy> [parseTaxonNames={false|true}]; - Loads a mapping file
Error: Command failed: Line 1: ‘mapType’ expected, got: ‘s’
Executing: use cViewer=INTERPRO2GO state=true;
Executing: use cViewer=KEGG state=false;
Executing: use cViewer=PGPT state=false;
Executing: load mapFile=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Colleen’s Forensics Analysis\megan-map-Feb2022.db’ mapType=MeganMapDB cName=SEED;
IOExceptionWithLineNumber: Line 1: ‘mapType’ expected, got: ‘s’
Command usage: load mapFile= mapType=<Accession|Synonyms|MeganMapDB> cName=<CARD|EC|EGGNOG|GTDB|INTERPRO2GO|KEGG|PGPT|SEED|Taxonomy> [parseTaxonNames={false|true}]; - Loads a mapping file
Error: Command failed: Line 1: ‘mapType’ expected, got: ‘s’
Executing: use cViewer=SEED state=true;
Executing: load mapFile=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Colleen’s Forensics Analysis\megan-map-Feb2022.db’ mapType=MeganMapDB cName=Taxonomy;
IOExceptionWithLineNumber: Line 1: ‘mapType’ expected, got: ‘s’
Command usage: load mapFile= mapType=<Accession|Synonyms|MeganMapDB> cName=<CARD|EC|EGGNOG|GTDB|INTERPRO2GO|KEGG|PGPT|SEED|Taxonomy> [parseTaxonNames={false|true}]; - Loads a mapping file
Error: Command failed: Line 1: ‘mapType’ expected, got: ‘s’
Executing: use cViewer=Taxonomy state=true;
Executing: update;

I downloaded and reinstalled the Megan twice and still the same errors.
Any help to resolve this would be greatly appreciated. Thanks.

-Mike

2

Update:

When I got into work today, I fired up my old computer (also running Windows 11). I used this computer to do the analysis of some diamond metagenomics files last spring using a previous version of MEGAN6 (6.22.2). Last spring I was able to load and analyze the meganized daa files but now I get the same errors described above when I try to load the same files! Fortunately, the student I am working with has a Windows 10 machine. So, we loaded MEGAN (6.24.20) on her machine and we were able to load the new meganized files and my old files just fine.

So the problem seems to be with Windows 11. Could there have been a recent update to the operating system that is incompatible with MEGAN? This is the only thing that makes sense to me because it worked fine on my Windows 11 machine last spring.

I hope this helps figure out the problem. We can use my student’s computer to analyze the files, but I would like to be able to use MEGAN on my computer also.

Thanks again!
-Mike

3

I think that the problem is that your directory names contain a single quote:

Executing: add file=‘C:\Users\mfoul\OneDrive\Documents\Metagenomics\Raj’s Erie Coke Analysis\DIAMOND-MEGAN Files\Meganized DAA Files\Diamond_ESO1A__DAA_output__forward.daa’;

Here, Raj’s Erie Coke Analysis is a problem. Unfortunately, MEGAN’s command parser interprets single quotes as indicators of single tokens and so it chokes. You can try escaping the single quote using ' or possibly \', but unfortunately, I’m not 100% confident that my code is going to be able to deal with that gracefully. You might have to rename the directories, I’m very sorry…

4

Daniel,

You are, of course, absolutely correct. And now I feel like a complete noob!

Thanks for getting back to me and for all that you do to keep Megan running for the community!

-Mike