problem in biom convert from text file to biom file

[Ping]

Hello,

I would like to convert an OTU table to BIOM format. I run the following command. There was no error, but the command did not run and did not generate a biom file.

The content of the text file is as follows:

# Constructed from biom file

#OTU ID	BS_0_1_1	BS_0_1_2	BS_0_1_3	BS_0_2_1
OTU0001	0	208	266	248
OTU0002	3343	5775	2565	4065
OTU0003	26975	11761	4825	9934
OTU0004	1327	1538	906	2
OTU0005	154	80	271	0
OTU0006	0	0	156	0
OTU0007	1403	7188	4325	166
OTU0008	1	4333	4150	95
OTU0009	6488	3124	2221	2348
OTU0010	482	692	947	688

.......................................................

BS_X_X_X is sample id. There is only count information for each OTU and no taxonomy column.

Does anybody know how to convert the text file to a biom file?

Thank you.

[Se Jin Song]

Hi Ping,

You're just missing one dash.

Pass

--to-hdf5 

instead of 

-to-hdf5

Best,

Se Jin

[Ping]

Hi Se Lin,

Thanks for your reply. I changed "-" to "--", but it still did not run. BTW, I am using Qiime 1.9.1.

Ping

[Se Jin Song]

Can you try 

--to-json

instead?

Thanks,

Se Jin

[Ping]

It did not work either. Not sure why it did not run.

[Ping]

The problem was the quotation mark. It works after I revised it.

Cheers,

Ping

[Se Jin Song]

Hi Ping, 

Glad you were able to figure it out!  Thanks for posting it.