How to import paired end illumina data?

[savan]

Hello, we are new to Qiime! Really need your help! We are trying to import data from a paired end Illumina data, which is already demultiplexed and in fastq format by Fastqprocessor.

We have files such as
Sample1_S10_L001_R1_001.fastq
Sample1_S10_L001_R2_001.fastq
Sample2_S10_L001_R1_001.fastq
Sample2_S10_L001_R2_001.fastq
…

We have followed the tutorial; use the code
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path FASTQDATA
–source-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path Fastqdata.qza

However, Qiime2 showed:
There was a problem importing FASTQDATA:
Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: ‘.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’

Could you please let me know how to fix it?

Thanks a lot!

[Nicholas_Bokulich]

Hi @savan,
See this post. Looks like your files aren’t gzipped, workarounds are suggested in that post.

I hope that helps!

[savan]

Thanks, Nicholas! I tried gzipped each fastq files to fastq.gz, however it shows:

There was a problem importing FASTQDATA:

Unrecognized file (FASTQDATA/Sample8_S10_L001_R1_001.fastq) for CasavaOneEightSingleLanePerSampleDirFmt.

Why just Sample 8 has problem? How can I fix it?

Thanks!

[savan]

Thank you guys! I just tried separated the fastq file and gzipped file to different folder, then it works! Now I have my .qza file finally!