Hi, I have an ASV table that I exported from QIIME2, batch-corrected using the SVA package in R, and now I want to import the table back into QIIME2 for reanalysis. Unfortunately, I’ve run into an issue and I’m not sure how to deal with it. I’m currently using QIIME 2018.4.
biom convert -i SVA_corrected_table_dada2_batches_merged_no_controls_formatted.txt -o SVA_corrected_table_dada2_batches_merged_no_controls_formatted.biom --table-type=“OTU table” --to-json
qiime tools import
When I run the above code, I get the following error message:
File “/home/marcolabuser/miniconda3/envs/qiime2-2018.4/lib/python3.5/json/decoder.py”, line 357, in raw_decode
raise JSONDecodeError(“Expecting value”, s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 4662605 (char 4662604)
An unexpected error has occurred:
Expecting value: line 1 column 4662605 (char 4662604)
See above for debug info.
This seems similar to what was posted here, but her error appeared in a different part of the file and the error was introduced by UNOISE. I haven’t used UNOISE with my data, so I’m wondering if something weird happened when I converted from .txt to .biom. I looked in both the .txt and .biom files but haven’t seen any obvious formatting issues. The files can be downloaded with my Google Drive links below:
Batch corrected .txt table: https://drive.google.com/open?id=1ZDAIlVic1sw9Lb1GNCn_xBg6fctV5FBa
Table after conversion to .biom format: https://drive.google.com/open?id=19ipz41yhNB71AwY2_SIIEHwpIOcSXQuB
Thanks for any help you can provide!