Problem trying to import my data with cassava

Technical Support
1

Hi,

I am trying to import my data with casava, as with manifest file does not work for me. I used this command:

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path /usr/home/biopatic/querejeta/mydata/amplicons_paired
–input-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path demux-paired-end.qza

There was a problem importing /usr/home/biopatic/querejeta/mydata/amplicons_paired:

Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’
But I get this error message:

My headings look like this:

CONTROL_S47_L001_R1_001.16S1F_5’-3’.fq.trimmed.paired.fastq.gz

CONTROL_S47_L001_R2_001.16S2R_5’-3’.fq.trimmed.paired.fastq.gz

CV10_S34_L001_R1_001.16S1F_5’-3’.fq.trimmed.paired.fastq.gz

CV10_S34_L001_R2_001.16S2R_5’-3’.fq.trimmed.paired.fastq.gz

CV11_S35_L001_R1_001.16S1F_5’-3’.fq.trimmed.paired.fastq.gz

CV11_S35_L001_R2_001.16S2R_5’-3’.fq.trimmed.paired.fastq.gz

CV12_S36_L001_R1_001.16S1F_5’-3’.fq.trimmed.paired.fastq.gz

CV12_S36_L001_R2_001.16S2R_5’-3’.fq.trimmed.paired.fastq.gz

Any ideas?

Thanks!

Nat

2

HI @Natalie,
Your filenames are not Casava format. I'd recommend sticking with the manifest format, especially as you are already asking for support with the manifest format in this topic:

It also looks like your files will match the Casava name conventions if you just remove "16S1F_5’-3’.fq.trimmed.paired." from each filename. You can give that a try and see if it imports — but if it fails then you will need to stick with manifest format, since that is the format your data are truly in!

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3

Thanks! worked out! :slight_smile:

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