Hi, so i was successful in making the emp-paired-end-sequences.qza. The challenge I have right now is semultiplexing. I am using the Atacama soil soil microbiome tutorial but I give getting the error plug in error from demux:
source activate (qiime2-2018.8) qiime2@qiime2core2018-8:~ source activate qiime2-2019.7
mkdir (qiime2-2019.7) qiime2@qiime2core2018-8:~ mkdir microbiome-data-analysis
(qiime2-2019.7) qiime2@qiime2core2018-8:~ mkdir paired-end-sequences
(qiime2-2019.7) qiime2@qiime2core2018-8:~ cd microbiome-data-analysis
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ mkdir paired-end-sequences
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime tools import \
--type EMPPairedEndSequences
--input-path emp-paired-end-sequences
--output-path emp-paired-end-sequences.qza
Usage: qiime tools import [OPTIONS]
Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/
for usage examples and details on the file types and associated semantic
types that can be imported.
Options:
--type TEXT The semantic type of the artifact that will be
created upon importing. Use --show-importable-types
to see what importable semantic types are available
in the current deployment. [required]
--input-path PATH Path to file or directory that should be imported.
[required]
--output-path ARTIFACT Path where output artifact should be written.
[required]
--input-format TEXT The format of the data to be imported. If not
provided, data must be in the format expected by the
semantic type provided via --type.
--show-importable-types Show the semantic types that can be supplied to
--type to import data into an artifact.
--show-importable-formats
Show formats that can be supplied to --input-format
to import data into an artifact.
--help Show this message and exit.
There was a problem with the command:
(1/1) Invalid value for "--input-path": Path "emp-paired-end-sequences" does
not exist.
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ mkdir emp-paired-end-sequences
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime tools import --type EMPPairedEndSequences --input-path emp-paired-end-sequences --output-path emp-paired-end-sequences.qza
Imported emp-paired-end-sequences as EMPPairedEndDirFmt to emp-paired-end-sequences.qza
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime demux emp-paired \
--i-seqs emp-paired-end-sequences.qza
--m-barcodes-file sample-metadata tsv
--m-barcodes-column BarcoseSequence
--p-no-golay-error-correction
--p-no-rev-comp-mapping-barcodes
--o-per-sample-sequences demux.qza
--o-error-correction-details demux-details.qza
There was an issue with loading the file sample-metadata 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): sample-metadata
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 2019.7.0 documentation
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime demux emp-paired --i-seqs emp-paired-end-sequences.qza --m-barcodes-file sample-metadata tsv --m-barcodes-column BarcoseSequence --p-no-golay-error-correction --p-no-rev-comp-mapping-barcodes --o-per-sample-sequences demux.qza --o-error-correction-details demux-details.qza
There was an issue with loading the file sample-metadata 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): sample-metadata
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 2019.7.0 documentation
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime demux emp-paired --i-seqs emp-paired-end-sequences.qza --m-barcodes-file sample-metadata.tsv --m-barcodes-column BarcodeSequence --p-no-golay-error-correction --p-no-rev-comp-mapping-barcodes --o-per-sample-sequences demux.qza --o-error-correction-details demux-details.qza
^C
Aborted!
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime demux emp-paired \
--m-barcodes-file sample-metadata.tsv
--m-barcodes-column barcode-sequence
--p-rev-comp-mapping-barcodes
--i-seqs emp-paired-end-sequences.qza
--o-per-sample-sequences demux.qza
--o-error-correction-details demux-details.qza^C
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime demux emp-paired --m-barcodes-file sample-metadata.tsv --m-barcodes-column barcode-sequence --p-no-rev-comp-mapping-barcodes --p-no-golay-error-correction --i-seqs emp-paired-end-sequences.qza --o-per-sample-sequences demux.qza
^C
Aborted!
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime demux emp-paired --m-barcodes-file sample-metadata.tsv --m-barcodes-column BarcodeSequence --p-no-rev-comp-mapping-barcodes --p-no-golay-error-correction --i-seqs emp-paired-end-sequences.qza --o-per-sample-sequences demux.qza
Usage: qiime demux emp-paired [OPTIONS]
Demultiplex paired-end sequence data (i.e., map barcode reads to sample
ids) for data generated with the Earth Microbiome Project (EMP) amplicon
sequencing protocol. Details about this protocol can be found at
Protocols and Standards : earthmicrobiome
Inputs:
--i-seqs ARTIFACT EMPPairedEndSequences
The paired-end sequences to be demultiplexed.
[required]
Parameters:
--m-barcodes-file METADATA
--m-barcodes-column COLUMN MetadataColumn[Categorical]
The sample metadata column containing the per-sample
barcodes. [required]
--p-golay-error-correction / --p-no-golay-error-correction
Perform 12nt Golay error correction on the barcode
reads. [default: True]
--p-rev-comp-barcodes / --p-no-rev-comp-barcodes
If provided, the barcode sequence reads will be
reverse complemented prior to demultiplexing.
[default: False]
--p-rev-comp-mapping-barcodes / --p-no-rev-comp-mapping-barcodes
If provided, the barcode sequences in the sample
metadata will be reverse complemented prior to
demultiplexing. [default: False]
Outputs:
--o-per-sample-sequences ARTIFACT
SampleData[PairedEndSequencesWithQuality]
The resulting demultiplexed sequences. [required]
--o-error-correction-details ARTIFACT ErrorCorrectionDetails
Detail about the barcode error corrections. [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).
--citations Show citations and exit.
--help Show this message and exit.
There was a problem with the command:
(1/1) Missing option "--o-error-correction-details". ("--output-dir" may
also be used)
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$ qiime demux emp-paired --m-barcodes-file sample-metadata.tsv --m-barcodes-column BarcodeSequence --p-no-rev-comp-mapping-barcodes --p-no-golay-error-correction --i-seqs emp-paired-end-sequences.qza --o-per-sample-sequences demux.qza --o-error-correction-details demux-details.qza
Plugin error from demux:
Debug info has been saved to /tmp/qiime2-q2cli-err-pbds1134.log
^[[A(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$
(qiime2-2019.7) qiime2@qiime2core2018-8:~/microbiome-data-analysis$
The qiime2 version is 2019.7