While importing my data, I encountered an error saying " These samples do not have matching pairs of forward and reverse reads" together with the IDs of the samples. I tried with a subset of the problematic samples, but it worked fine. Any ideas what the problem could be?
While importing my data, I encountered an error saying " These samples do not have matching pairs of forward and reverse reads" together with the IDs of the samples. I tried with a subset of the problematic samples, but it worked fine. Any ideas what the problem could be?
Could you tell me a little more about how your imported your data? Like, what command did you run and what files did you pass? Did your sequencing core or another researcher do any other filtering on the data before you imported it using Qiime 2?
So I am importing the data using a manifest file with this command:
qiime tools import
βtype βSampleData[PairedEndSequencesWithQuality]β
βinput-path manifest.tsv
βoutput-path demux.qza
βinput-format PairedEndFastqManifestPhred64V2
I have already imported other files (from other cohorts in the same study) from the same sequencing center with a similar approach. I also tried with a toy subset of my files with a manifest and it worked just fine.
Because you are imported paired reads, Qiime assumes you have a forward and reverse file for each sample. It also assumes that the forward and reverse file has the same number of reads.
Looks like some of the files are missing reads from one or both ends. Lots of things could cause this, including a partial download, or a prefiltering step that removed reads from one file but not the other. (Some programs also check that the read names match, but I'm not sure if that's checked here.)
This is great! We know the script it working on your system. Now we just to figure out which files are missing reads and why.
Thank you.
The thing that I donβt understand is that, I got the error for the following samples (which are not all of my files, but a big part of them):
{β13β, β34β, β33β, β12β, β1β, β38β, β32β, β17β, β24β, β15β, β10β, β18β, β19β, β35β, β26β, β30β, β27β, β22β, β21β, β29β, β14β, β37β, β36β, β16β, β20β, β11β, β3β, β28β, β25β, β31β, β23β, β2β}
However, when I tried with the first five samples (β13β, β34β, β33β, β12β, β1β), it worked just fine. So, I was wondering what could be the reason that they popped up as problematic when importing all of the files, but they were fine separately?
Because when the error specifies file IDs, I assume there should be a problem with all of the reported IDs.
You could possibly have an βoff-by-oneβ type of error, which basically cascades. Could you share your manifest file for us, maybe we can tune up the validation routine a bit to provide a cleaner error message. Thanks!
Yes, the sequencing center has already done some quality filtering (trimming, removal of adapters,β¦). However, I havenβt had any problems with the reads of other cohorts that have been sequenced in the same center.