Hello, I have issue when I run the dada2 (Qiime version: 2022-11). I used the script below,
qiime dada2 denoise-paired
--i-demultiplexed-seqs ./paired-end-demux.qza
--p-trim-left-f 10
--p-trunc-len-f 290
--p-trim-left-r 10
--p-trunc-len-r 250
--p-max-ee-f 2
--p-max-ee-r 2
--p-n-threads 0
--o-table ./dada2_table.qza
--o-representative-sequences ./dada2_repseqs.qza
--o-denoising-stats ./dada2_stats.qza
qiime metadata tabulate
--m-input-file ./dada2_stats.qza
--o-visualization ./dada2_stats.qzv \
qiime feature-table summarize
--i-table ./dada2_table.qza
--m-sample-metadata-file ./mapping.txt
--o-visualization ./dada2_table.qzv
qiime feature-table tabulate-seqs
--i-data ./dada2_repseqs.qza
--o-visualization ./dada2_repseqs.qzv
mapping.txt (71 Bytes)
I used the Keemei to check the format of mapping file, it shows no problems. the scripts I have used for multiple times, it didn't give error before.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-ls2o0dfw.log
There was an issue with loading the file ./dada2_stats.qza as metadata:
Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): ./dada2_stats.qza
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Find details on QIIME 2 metadata requirements here: Metadata in QIIME 2 — QIIME 2 2022.11.1 documentation
Usage: qiime feature-table summarize [OPTIONS]
Generate visual and tabular summaries of a feature table.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
PresenceAbsence] The feature table to be summarized. [required]
Parameters:
--m-sample-metadata-file METADATA...
(multiple The sample metadata.
arguments will
be merged) [optional]
Outputs:
--o-visualization VISUALIZATION
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Examples:
### example: feature table summarize
qiime feature-table summarize
--i-table feature-table.qza
--o-visualization table.qzv
There was a problem with the command:
(1/1) Invalid value for '--i-table': dada2_table.qza does not exist.
Usage: qiime feature-table tabulate-seqs [OPTIONS]
Generate tabular view of feature identifier to sequence mapping, including
links to BLAST each sequence against the NCBI nt database.
Inputs:
--i-data ARTIFACT FeatureData[Sequence | AlignedSequence]
The feature sequences to be tabulated. [required]
Outputs:
--o-visualization VISUALIZATION
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Examples:
### example: feature table tabulate seqs
qiime feature-table tabulate-seqs
--i-data rep-seqs.qza
--o-visualization rep-seqs.qzv
There was a problem with the command:
(1/1) Invalid value for '--i-data': dada2_repseqs.qza does not exist.
paired-end-demux.qzv (315.6 KB)
Thanks for your help.