Hello, I am relatively new to qiime. I am using the version QIIME2 (2018.8) and I am facing problems with importing the data.
The data is paired end sequencing data generated from HiSeq-PE 250 for 30 samples. I have two separate file one for forward and one for reverse in fastq.gz format.
I have tried all the tutorials but somehow I am not able to solve my issue. It would be great if someone can help me.
Where are your barcodes? If they are part of the sequences, you should follow this tutorial. If they are in separate barcode files, you should use the EMP paired end format described in the importing tutorial.
I have 30 samples, each with a file which has raw tags after reads merging. I combined all these fastq files into one fastq file and then converted into merged.fastq.gz format.
At this point I have one merged.fastq.gz and a metadata file.
My files were originally names as:
DMP06592_L1_AF2.raw_1.fq.gz
DMP06592_L1_AF2.raw_2.fq.gz …
so I also created another directory named raw_pair_end_reads_demultiplexed with all forwards and reverse reads named as above and I used the following command:
@pmehta, thank you for providing such a detailed description of your process. I’m pretty new here myself, and it helps so much!
These errors both seem to point at incorrectly-formatted filenames. Is there any chance your reverse.fastq.gz is misspelled, named reverse.fq.gz, or there’s some similar typo?
Background Information: qiime tools import is looking through your --input-path directories for files that meet specific naming conventions. The error messages you’re receiving describe the exact pattern of characters the command is looking for. If the names of your files don’t match the expected format for the type of Artifact you’re trying to create, import won’t be able to find them.
Hi@pmehta!
Have you looked at the tutorial for importing files using a manifest.tsv file. I guess this should work in importing your two .gz files into qiime2 for downstream analysis.