No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>
I am new to qiime2.
- I am getting a following error when importing my data.
There was a problem importing MANIFESTSheet1.tsv:
MANIFESTSheet1.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:
'forward-absolute-filepath' is not a column in the metadata. Available columns: 'absolute-filepath''
- I have 3 samples AC, NC and BS (each with R1 and R2 reads) with no barcode sequences. my sample reads are named as follows
AC1_R1.fq.gz
AC2_R2.fq.gz
BS1_R1.fq.gz
BS2_R2.fq.gz
NC1_R1.fq.gz
NC2_R2.fq.gz - Is there a issue in my manifest file. manifest file is in tsv format.
sample-id absolute-filepath
AC1 /root/Data/reads/AC1_R1.fq.gz
AC2 /root/Data/reads/AC2_R2.fq.gz
BS1 /root/Data/reads/BS1_R1.fq.gz
BS2 /root/Data/reads/BS2_R2.fq.gz
NC1 /root/Data/reads/NC1_R1.fq.gz
NC2 /root/Data/reads/NC2_R2.fq.gz - import command used are
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path MANIFESTSheet1.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2
Since you are using paired-end data, you will need to adjust your manifest file so that you have both a forward-absolute-filepath
and a reverse-absolute-filepath
for each sample. Check out this portion of the importing tutorial and feel free to stop back by with any other questions
You should also change the extensions on your files from *.fq.gz
to *.fastq.gz
.
Thanks @Keegan-Evans did the changes you suggested and the problem is solved
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