Hi, wondering if anyone can help me.
I'm running Qiime2-2023.2, Conda environment via my Uni HPC cluster on Linux.
I've downloaded some SRA data using SraToolKit and Sradownloader, and have managed to create a demux qza using a manifest file. So far so good.
Then I've gone ahead with trimming the primers, as provided in the research paper.
Command used was:
qiime cutadapt trim-paired
The verbose log I got showed that the trimming appears to be working well, then all of a sudden I get this error:
Command line parameters: --cores 1 --error-rate 0.1 --times 1 --overlap 3 --minimum-length 1 -q 0,0 --quality-base 33 -o /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-z4huq7ej/SRR12115264_105_L001_R1_001.fastq.gz -p /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-z4huq7ej/SRR12115264_225_L001_R2_001.fastq.gz --front ACTCCTACGGGAGGCAGCA -G GGACTACHVGGGTWTCTAAT --match-read-wildcards --discard-untrimmed /tmp/qiime2/rjs202/data/95092ed2-783f-4794-b454-6abbc734b63c/data/SRR12115264_105_L001_R1_001.fastq.gz /tmp/qiime2/rjs202/data/95092ed2-783f-4794-b454-6abbc734b63c/data/SRR12115264_225_L001_R2_001.fastq.gz
Processing paired-end reads on 1 core ...
ERROR: Error in sequence file at unknown line: Reads are improperly paired. Read name 'SRR12115264.30992 30992/2' in file 1 does not match 'SRR12115264.1 1/2' in file 2.
So it looks like the naming convention for the paired reads has gone awry at this point, but I can't understand why or how to fix it, unless I just remove this one sample from the batch and hope that the others work ok.
I have rechecked my manifest file and it is correctly pointing to the right pairs, and the naming conventions used do not differ as far as I can see. I wonder if it is something to do with how the SRA files were downloaded from the SRA but that is a bit beyond my knowledge.
Thanks in advance for any help anyone can offer. I know similar threads have been posted on this subject, but couldn't see a problem that was exactly like mine.