error occured whemn importing data

User Support
#1

No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

data import error
#2
#3

I am new to qiime2.

  1. 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''

  1. 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
  2. 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
  3. import command used are
    qiime tools import
    --type 'SampleData[PairedEndSequencesWithQuality]'
    --input-path MANIFESTSheet1.tsv
    --output-path paired-end-demux.qza
    --input-format PairedEndFastqManifestPhred33V2
#5

@priti,

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 :slightly_smiling_face:

#6
#7

@priti,

You should also change the extensions on your files from *.fq.gz to *.fastq.gz.

#8

Thanks @Keegan-Evans did the changes you suggested and the problem is solved

1 Like
#9

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