Problem while loading BIOM file in STAMP

k_a_r_o_l · 04-20-2017, 04:54 AM

Hello,

When I am loading my BIOM file in STAMP everything goes well and I am able to generate .spf file but when I want to open this file I get an error message:

"Field to correctly parse lines: 1298"

So I have chacked and it looks like this (I'm showing lines 1296 -1299)

k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__ g__ s__ 463289 7.0 3.0 35.0 233.0

k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__ g__ s__ 228232 2.0 14.0 3.0 0.0

k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__S24-7 g__ s__ New.ReferenceOTU78 0.0 3.0 0.0 1.0

k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__ g__ s__ New.ReferenceOTU79 1.0 2.0 4.0 0.0

I see that starting from the line 1298 in "Observation Ids" collumn I am getting New.ReferenceOTUxxx and I have this parameter to the end of my file. Before line 1298 I have Observation Ids in numbers.

What can I do or change? Maybe I should change something during my Qiime analysis?

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04-20-2017, 04:54 AM	#1
k_a_r_o_l Junior Member Location: Warsaw Join Date: Mar 2014 Posts: 9	Problem while loading BIOM file in STAMP Hello, When I am loading my BIOM file in STAMP everything goes well and I am able to generate .spf file but when I want to open this file I get an error message: "Field to correctly parse lines: 1298" So I have chacked and it looks like this (I'm showing lines 1296 -1299) k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__ g__ s__ 463289 7.0 3.0 35.0 233.0 k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__ g__ s__ 228232 2.0 14.0 3.0 0.0 k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__S24-7 g__ s__ New.ReferenceOTU78 0.0 3.0 0.0 1.0 k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__ g__ s__ New.ReferenceOTU79 1.0 2.0 4.0 0.0 I see that starting from the line 1298 in "Observation Ids" collumn I am getting New.ReferenceOTUxxx and I have this parameter to the end of my file. Before line 1298 I have Observation Ids in numbers. What can I do or change? Maybe I should change something during my Qiime analysis?