Thanks in advance to helping me out
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path 324renamed --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
(please correct me if wrong here, not sure if the format type was correct)
- I ran the summarize function but got an error
qiime demux summarize --i-data demux-paired-end.qza --o-visualization demux-summary.qzv
Error -3 while decompressing data: invalid bit length repeat
Debug info has been saved to /tmp/qiime2-q2cli-err-yivwv3bd.log.
- Then ran the dada plug-in just to see if it would wor
qiime dada2 denoise-single --p-trim-left 13 --p-trunc-len 150 --i-demultiplexed-seqs demux-paired-end.qza --o-representative-sequences rep-seqs.qza --o-table table.qza
An error was encountered while running DADA2 in R (return code -9)
please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-fr8i_7db.log.
Please advise me if there’s something I am doing wrong
Everything you’ve done looks great, however I suspect there is something wrong with the original
fastq.gz data that you imported.
demux summarize is the first step where QIIME 2 starts really reading those files and it looks like something went wrong when they were compressed. I noticed your
324renamed do you have original copies of your source data elsewhere? Were they already
fastq.gz or did you have to gzip them yourself?
I had to rename fastq.gz files to follow the naming convention of "01_L00_R1(or 2)_001"
See attached screenshot of the directory where the files are located.
Yes, I do have the original files elsewhere, I just copied and renamed into "324renamed"
The original files were all gzipped on arrival - in fact they were tarred and I had to untar them
What do you suggest I do now? recopy and rename the files?
Also, I am using a cluster for the analysis but that shouldn't matter much
Thanks so much!
You could try running
gunzip -t *.fastq.gz which will check that each file is compressed correctly.
If you get no results from that command that will mean that everything is fine with your sequence data.
In which case, perhaps try importing again like before. (You should have gotten a different error if the data hadn’t finished being added to the
.qza with the import, but it doesn’t hurt to try again.)
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.