ERROR in loading BIOM file

User Questions
1

Hello,

I am using MEGAN 6 (6.7.1) and MEGAN 5 (5.11.3) on Ubuntu system. Loading BIOM file into these software used to be well. But now it keeps showing: Error: Execute failed: java.io.IOException: [F cannot be cast to [I.

Messages in MEGAN 6:
Executing: import format=biom file=’/media/yichao/Temporary/Amplicon_Quarries_Data/L1/otu_table_k__Bacteria_json_cleaned_megan.biom’ type=‘Taxonomy’;
{"co
Importing data from BIOM file
[F cannot be cast to [I Command usage: import format=biom file=<fileName> [type={TAXONOMY|KEGG|SEED|UNKNOWN}]; - Import samples from a table in BIOM 1.0 (JSON) format (see http://biom-format.org/documentation/format_versions/biom-1.0.html)
[F cannot be cast to [I
Error: Execute failed: java.io.IOException: [F cannot be cast to [I

Message in MEGAN 5:
Executing: import format=biom file=’/media/yichao/Temporary/Amplicon_Quarries_Data/L1/otu_table_k__Bacteria_json.biom’ type=‘taxonomy’;
Importing data from BIOM file
Command usage: import format=biom file= [type={TAXONOMY|KEGG|SEED|UNKNOWN}]; - Import samples from a table in BIOM 1.0 format (see http://biom-format.org/documentation/format_versions/biom-1.0.html)
java.util.LinkedHashMap cannot be cast to com.google.gson.internal.StringMap

Any advice would be greatly appreciated!

Best Regards,
Yichao

2

Thanks for the bug report, I have located the problem and it will be fixed in 6.7.3

3

Thanks Daniel:smiley:

4

Hi all

I am facing the same problem, I’ve just installed Megan6 and updated Java, but the error message is there whenever I try to open a .biom file…
I don’t know what I am doing wrong.
Error message:
Version MEGAN Community Edition (version 6.8.8, built 26 May 2017)
Copyright © 2017 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
This is free software, licensed under the terms of the GNU General Public License, Version 3.

Opening startup files
Loading ncbi.map: 1,601,128
Loading ncbi.tre: 1,601,131
Induced tree has 1,601,131 of 1,601,131 nodes
Executing: open file=‘C:\Users\mcerqueira\Downloads\ERR1746143_FASTQ_otu_table_json.biom’;
File has unknown type: C:\Users\mcerqueira\Downloads\ERR1746143_FASTQ_otu_table_json.biom
Command usage: open file= [readOnly={false|true}]; - Open a MEGAN file (ending on .rma, .meg or .megan)
File has unknown type: C:\Users\mcerqueira\Downloads\ERR1746143_FASTQ_otu_table_json.biom
Error: Execute failed: java.io.IOException: File has unknown type: C:\Users\mcerqueira\Downloads\ERR1746143_FASTQ_otu_table_json.biom
Executing: open file=‘C:\Users\mcerqueira\Downloads\ERR1746143_FASTQ_otu_table_hdf5.biom’;
File has unknown type: C:\Users\mcerqueira\Downloads\ERR1746143_FASTQ_otu_table_hdf5.biom

Thanks for your help.

Teresa

5

Use the following menu item: File->Import->Biom1 Format…