Error in biom convert with mothur generated biom files

I have generated some biom files with make.biom and have problems to convert these files with the biom convert command. My biom files looks like this:

“format”: “Biological Observation Matrix 0.9.1”,
“format_url”: “”,
“type”: “OTU table”,
“generated_by”: “mothur1.35.1”,
“date”: “Thu Jun 25 16:25:34 2015”,
{“id”:“Otu0001”, “metadata”:{“taxonomy”:[“Bacteria”, “Bacteroidetes”, “Bacteroidia”, “Bacteroidales”, “Prevotellaceae”, “Prevotella”], “bootstrap”:[100, 100, 100, 100, 100, 100]}},
{“id”:“Otu0002”, “metadata”:{“taxonomy”:[“Bacteria”, “Bacteroidetes”, “Bacteroidia”, “Bacteroidales”, “Prevotellaceae”, “Prevotella”], “bootstrap”:[100, 100, 100, 100, 100, 100]}},
{“id”:“Otu0003”, “metadata”:{“taxonomy”:[“Bacteria”, “Firmicutes”, “Clostridia”, “Clostridiales”, “Ruminococcaceae”, “Faecalibacterium”],
{“id”:“1515801”, “metadata”:null},
{“id”:“1515803”, “metadata”:null},
{“id”:“1515803d”, “metadata”:null}
“matrix_type”: “sparse”,
“matrix_element_type”: “int”,
“shape”: [1726,3],
“data”: [[0,0,6958],


The error message with the biom convert command is:

qiime@qiime-190-virtual-box:~$ biom convert -i Desktop/Shared_Folder/V3V5_Greengenes_OTU.BIOM -o V3V5_Greengenes_OTU.txt --to-tsv
Traceback (most recent call last):
File “/usr/local/bin/pyqi”, line 184, in
optparse_main(cmd_obj, argv[1:])
File “/usr/local/lib/python2.7/dist-packages/pyqi/core/interfaces/optparse/”, line 275, in optparse_main
result = optparse_cmd(local_argv[1:])
File “/usr/local/lib/python2.7/dist-packages/pyqi/core/”, line 38, in call
cmd_input = self.input_handler(in, *args, **kwargs)
File “/usr/local/lib/python2.7/dist-packages/pyqi/core/interfaces/optparse/”, line 194, in _input_handler
File “/usr/local/lib/python2.7/dist-packages/biom/interfaces/optparse/”, line 42, in load_biom_table
return parse_biom_table(table_f)
File “/usr/local/lib/python2.7/dist-packages/biom/”, line 310, in parse_biom_table
t = Table.from_json(json.load(fp), input_is_dense=input_is_dense)
File “/usr/lib/python2.7/json/”, line 278, in load
File “/usr/lib/python2.7/json/”, line 326, in loads
return _default_decoder.decode(s)
File “/usr/lib/python2.7/json/”, line 366, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File “/usr/lib/python2.7/json/”, line 382, in raw_decode
obj, end = self.scan_once(s, idx)
ValueError: Invalid \escape: line 2 column 15 (char 16)

Do you have any suggestions?

Thanks in advance


It looks like qiime is complaining because the filename C:\Users\afrontzek\Documents\Mothur_Daten\RV_Metabiom_V1V3_1\ is from a windows machine and contains windows ‘’ slash characters. Thanks for reporting this issue. We will remove the path from the filenames for our next release. As a workaround try editing the line to look like:

“format”: “Biological Observation Matrix 0.9.1”,