Hi,
We have already demultiplexed 250bp pairedend samples of 124 all sequenced on one lane. I used the following command to import it ( not sure about source-format since couldn’t find the detailed explanation of all importable-types)
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path fastq
–source-format CasavaOneEightLanelessPerSampleDirFmt
–output-path demux-paired-end.qza
This runs with no error and then when I want to continue with demux summarize:
Summarize demuxed data
qiime demux summarize
–i-data demux-paired-end.qza
–o-visualization demux-paired-end.qzv
I get the following error:
Plugin error from demux:
[Errno 2] No such file or directory: ‘/var/folders/wx/rk1376mx19j5w4l4czbdzs11lq284c/T/qiime2-archive-ydpb09_c/f92fbb59-3a31-4f66-9285-a70764f4b722/data/MJneg-control_S121_L001_R1_001.fastq.gz’
Debug info has been saved to /var/folders/wx/rk1376mx19j5w4l4czbdzs11lq284c/T/qiime2-q2cli-err-5sncf3lo.log
I was able to export the data and it seams like all the files are there.the MANIFEST file content starts with:
sample-id,filename,direction
MJneg-control_S121,MJneg-control_S121_L001_R1_001.fastq.gz,forward
MJneg-control_S121,MJneg-control_S121_L001_R2_001.fastq.gz,reverse
MJpos-control_S122,MJpos-control_S122_L001_R1_001.fastq.gz,forward
MJpos-control_S122,MJpos-control_S122_L001_R2_001.fastq.gz,reverse
…
…
…
I also tried to run dada2:
Denoise the data. Looking at the quality plots , half of the samples do not need trimming, but some need around ranging bw 350-450.
250 bp Paired end reads
qiime dada2 denoise-single
–i-demultiplexed-seqs demux-paired-end.qza
–p-trim-left 0
–p-trunc-len 450
–o-representative-sequences rep-seqs-dada2.qza
–o-table table-dada2.qza
throws the following error:
Plugin error from dada2:
A path specified in the manifest does not exist or is not accessible: /var/folders/wx/rk1376mx19j5w4l4czbdzs11lq284c/T/qiime2-archive-njbviyfg/f92fbb59-3a31-4f66-9285-a70764f4b722/data/MJneg-control_S121_L001_R1_001.fastq.gz
Debug info has been saved to /var/folders/wx/rk1376mx19j5w4l4czbdzs11lq284c/T/qiime2-q2cli-err-fbzuql0u.log
So it’sa similar issue of not being able to locate fastq files in the artifact. Is this some type of a bug or what am I doing wrong. Please HELP…
Thanks