Plugin Error from qiime demux and dada- invalid bit length repeat

Thanks in advance to helping me out

  • I am running q2cli version 2017.7

  • I had demultiplexed paired sequences which seemed to import successfully using:

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

Hey @mcoker,

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 --input-path says 324renamed do you have original copies of your source data elsewhere? Were they already fastq.gz or did you have to gzip them yourself?

thanks, Evan

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!

Hey @mcoker,

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.)

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