Hello all,
I'm using Qiime2: qiime2-2021 with conda.
I already used the dada2 script with no problems but now I have one with a new dataset.
I have a problem with the qiime dada2 denoise-paired step.
When I do this step:
qiime dada2 denoise-paired
--i-demultiplexed-seqs Rhipicephallus-demux2.qza
--p-trim-left-f 5
--p-trim-left-r 5
--p-trunc-len-f 194
--p-trunc-len-r 200
--verbose
--p-n-threads 20
--output-dir dada3
I have the following error message appearing.
Le chargement a nécessité le package : Rcpp
Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
These are the errors (up to 5) encountered in individual cores...
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 11940, 36323.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 9554, 37532.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 37532, 9554.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 5961, 29803.
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 29803, 5961.
Exécution arrêtée
So I looked in the forum for help in this topic: Error in filtering using DADA2
I tried do do the following lines:
qiime tools export Rhipicephallus-demus2.qza --output-dir debugging
cd debugging
for f in *.fastq.gz; do r=(( (gunzip -c $f | wc -l | tr -d '[:space:]') / 4 )); echo $r $f; done
But the following error message appeared:
Usage: qiime tools export [OPTIONS]
Exporting extracts (and optionally transforms) data stored inside an
Artifact or Visualization. Note that Visualizations cannot be transformed
with --output-format
Options:
--input-path ARTIFACT/VISUALIZATION
Path to file that should be exported [required]
--output-path PATH Path to file or directory where data should be
exported to [required]
--output-format TEXT Format which the data should be exported as. This
option cannot be used with Visualizations
--help Show this message and exit.
There was a problem with the command:
(1/1?) no such option: --output-dir
/var/spool/slurmd/job843371/slurm_script: ligne 63 : cd: debugging: Aucun fichier ou dossier de ce type
gzip: *.fastq.gz: No such file or directory
Why is it not working ? How can I know where is the problem in my data ?
When I looked at my demux.qzv file, all the counts were good in "Per-sample sequence counts".
Thank you in advance for your help.