I have finished running DADA2 and am now in the process of trying to summarize and visualize my feature table. To do this, I have to input my metadata (QIIME1's mapping) file, however when I do so, I am getting an error saying that my metadata file must be encoded as UTF-8 or ASCII.
I checked the file type using code below:
(qiime2) u12923-2k3:2018_SkinSampling_rerun u12923$ file -I mapping_skinABiL.tsv
mapping_skinABiL.tsv: text/plain; charset=iso-8859-1
as you see, the character type is not correct. My computer is a MAC so when I create this metadata file, I start in excel and save the final product as as .tsv file. I have attached the metadata file. I did validate it in keemei and I get warnings because my sample ids have "_" instead of "-", however I cannot change this because when I imported my sequences, they included the sample ids (ex: "G139_2_R1.fastq") as part of the file name. Can you help me figure out why I continue to get this error. I've even tried rerunning with sample ids changed (ex: G139-2) in the metadata file, but I get the same error. I then saved the metadata file as a UTF-8 csv file and changed the extension to .tsv and used that as the metadata input in the following code and get the following error:
(qiime2) u12923-2k3:2018_SkinSampling_rerun u12923$ qiime feature-table summarize --i-table first_analysis/02_DADA2/dada2_table.qza --o-visualization first_analysis/02_DADA2/dada2_table.qzv --m-sample-metadata-file mapping_skinABiL_utf.tsv
There was an issue with loading the file mapping_skinABiL_utf.tsv as metadata:
Found unrecognized ID column name '\ufeff#SampleID,BarcodeSequence,LinkerPrimerSequence,BarcodeName,ProjectName,Sample_ID,Subject_ID,age_years,Sampling_method,organism,organism_part,race,sex,ethnic_group,material_entity,assay_type,library_source,library_selection,library_strategy,library_layout,assay_platform,Vendor_name,DNA_extraction_date,Library_preparation_date,Sequence_date,Description' while searching for header. The first column name in the header defines the ID column, and must be one of these values:
Case-insensitive: 'feature id', 'feature-id', 'featureid', 'id', 'sample id', 'sample-id', 'sampleid'
Case-sensitive: '#OTU ID', '#OTUID', '#Sample ID', '#SampleID', 'sample_name'
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Please help me identify why I am continuously getting an error for my metadata file.