import fastq files

i’m trying to import my fastq files using Casava 1.8 paired-end demultiplexed fastq.
some of my files are fastq.gz with the ordination you describe in qiime docs: L2S357_15_L001_R1_001.fastq.gz.
but some of my file are fastq and looks like this 709-502-NJ103-114D_R2_001.fastq.

I tried to run the command anyway but I got an error
There was a problem importing Bariatric_Fastqs/Bariatric_Fastqs:
“Unrecognized file (Bariatric_Fastqs/Bariatric_Fastqs/701508NJ8102D_R2_001.fastq) for CasavaOneEightSingleLanePerSampleDirFmt.”

I assume that the reason is the file names. do you have any suggestion how can I solve it?


Hi @Adi!

It looks like your filenames are missing the barcode segment and the lane number segment, so our import isn’t working, since it counts backwords from the 001 segment to identify the sample ID correctly.

You’ll want to either import using a fastq manifest format which will spell out the sample IDs and filepaths directly, or find a way to add the missing barcode and lane segments to your filepaths. I would probably recommend the former, so that you don’t accidentally rename files the wrong way (potentially losing data), but if you are comfortable with Bash, the latter is certainly easier.

1 Like