I want to use DADA2 to do quailty control, and to do the community analysis.With my own script, i can get the 16S sequence with the quailty. However, when I set these data as input, I got some problem. Here is the error message:
There was a problem importing sample_hyh.csv:
/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-kuws7b/FH60-5-MG-2_5_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Quality score length doesn't match sequence length for record beginning on line 5
The version I used is version 2023.5.0., and it was installed by conda.
The commands I ran shows follows:
qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path sample_hyh.csv
--output-path single-demux.qza
--input-format SingleEndFastqManifestPhred33
Here is the sample_hyh.csv sample_hyh.csv (3.7 KB)
And this is one of my input data (I have use gzip -c to compress the sequence extract from metagenomic data): FH61-3-MG-2_1.16SQ.fastq.gz (4.2 KB) FH61-3-MG-2_1.16SQ.fastq (101.7 KB)
Really than you for your help!
I modified my scripts, with the sequence in the second line and the quality in the fourth line.
However, I still got some error message:
There was a problem importing sample_hyh.csv:
/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-hx0g0efi/FH60-5-MG-2_5_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Quality score length doesn't match sequence length for record beginning on line 5
I am not sure what the issue is, as I have been able to import both of these files into QIIME 2023.5 & 2023.7 without issue. Perhaps there is something wrong with your install or system?