Hello qiime team,
I have been trying to import my data into qiime but its giving me errors and I’ve tried different things.
My data can be found at:
My data is MiSeq Illumina dual index paired end sequences in the FASTQ format. I am trying to import them into qiime. There are four files that were generated by Illumina: I1, I2 (corresponding to the barcodes stripped from the sequences from demultiplexing) and R1, R2 (corresponding to the forward and reverse sequences). I have been trying to import the data and tried different manifest files, maybe there is a part that i am missing or overlooking. Thank you for your time and patience.
I was using the following script and other variations of this:
qiime tools import
–output-path paired-end-demux.qza \
There was a problem importing rawsequences:
rawsequences/B2_S150_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Header on line 1 is not FASTQ, records may be misaligned
however to my understanding B2 is a fastq file
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path rawsequences --output-path paired-end-demux.qza --input-format FastqGzFormat
An unexpected error has occurred:
No transformation from <class ‘q2_types.per_sample_sequences._format.FastqGzFormat’> to <class ‘q2_types.per_sample_sequences._format.SingleLanePerSamplePairedEndFastqDirFmt’>
See above for debug info.
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path manifest1.tsv --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2
There was a problem importing manifest1.tsv:
/tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-sk30d3vy/1C_8_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Header on line 5 is not FASTQ, records may be misaligned
to my understanding 1C_8_L001_R1_001.fastq.gz is in FastqGzFormat file