Hi,
I am trying to but was unable to import fastq file into qiime2 (qiime2-2018.6). The data are for v4 region of 16S. For each patient, I have two files, with one for forward and one for reverse. All files are decompressed. There are no barcode files. The files are stored in a folder called Yang / Yang2, and the file name is like:
AB2S74_01_L001_R1_001.fastq
AB2S76_02_L001_R1_001.fastq
AB2S74_01_L001_R2_001.fastq
AB2S76_02_L001_R2_001.fastq
Part of the content of the first file (AB2S74_01_L001_R1_001.fastq) is shown below:
@M00307:30:000000000-B3PKC:1:1101:14934:1406 1:N:0:GGAGCTAC+GAGCCTTA
ATTGGGCGTAAAGTGAGCGTAGACGGACTTGCAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGTAGGTCTAGAGTGCTGGAGAGGTAAGTGGAATTCCTCGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTA
+
AABBBBFBBBBBGGGGFGEEFE2FEG2AAGGGH5GFGFFGFFGGGHHFHHFFGGGEEHFHHHGGFGCEGHHHHHGHHEFFGHGH4GFBFG3G?GFGFHHGFG3?EBGFHGHHFHHHHHH3CFGGBGHCGGCEDGGGGGDFGFGHHG1FB<GDECG<GGEHHGHGGGGCGHGGAFG/BBFBBFCEFGGFGGGGFE…;FFFFA;9…AB.;;;;DEA.AFF?.;?AFFFFF9;BFFFFEBF
@M00307:30:000000000-B3PKC:1:1101:15666:1410 1:N:0:GGAGCTAC+GAGCCTTA
ATTGGGTTTAAAGTGCATGTAGGCGGTTATCTAAGCTTGGTGTGAAAGGCAGGGGCTCCACTCCTGGACTGCATTGAGAACTGGATGACTAGAGTTACTGAAGTGAAATCAGAATTCCAGGTGTAGGGGTGAAATCTGTAGATATCTGGAAGAATACCAATGGCGAAGGCAGGTTTCAGGCAGATAACTGACGCTGAGGTGCGAAGGTGCGGGGAGCAAACGGGATTAGATACCCGCGTA
+
AABBBBAABFFFGGGCGGGFGFHHGGEE2GFGGGHHDGFEGGHGGAFFFH11EGGEE11BGHFHFGFHFHEF3FFF@3FFFHHH?GGBFG4B3F@G44F4@FGGGFFHGHHF?FGHHHFHH3FF?DGGGAC??GHFGHFFH@GHHGGGH2GHFGDGFHF1FGHFC/<AEFCDGCGHE==GGFFAGFFHGFC;AED?.CFHHFGE-;.;;9BFAD;BFEBB9DDFDFFFBBF/BBFDBAFA
@M00307:30:000000000-B3PKC:1:1101:17304:1441 1:N:0:GGAGCTAC+GAGCCTTA
ACTGGGCGTAAAGAGAGCGTAGACGGCAGAGCAAGTCTGATGTGAAAGGCAGGGGCTCAACCCCTGGACTGCATTGGAAACTGTTCGGCTTGAGTGCCGGAGAGGGAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGACGGCAACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCAGTA
I am trying to use Casava 1.8 paired-end demultiplexed fastq to import the data according to the QIIME2 tutorial with the following command:
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path Yang/Yang2 --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
However, I got the following error message:
Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’
So my questions are:
- How to fix this problem?
- I expect the length should be around 150 bp for either forward or reverse because these are paired-end data (v4 region). However, I found the long is around 250 bp. I don’t why?
Any suggestions are greatly appreciated!
James