Last login: Fri Jul 5 16:04:40 on ttys002 (base) My-Mac:~ danaroberts$ ls Applications Library Public convert_fastq.sh Desktop Movies Send Registration v2.13.4.tar.gz Documents Music Sites vsearch-2.13.4 Downloads Pictures VirtualBox VMs (base) My-Mac:~ danaroberts$ cd Desktop (base) My-Mac:Desktop danaroberts$ ls Allium Leafminer BumbleBeeGuideEast2011.pdf EPG ARS Parlier 2019 ESA17_PDF.pdf IMG_0672.jpg Mariam's pipeline.txt PA Police background check 20may19.pdf Pennsylvania Access To Criminal History - Record Check Invoice copy.pdf SAS 9.4 mac SAS x64 Screen Shot 2019-05-20 at 8.23.02 PM.png Screen Shot 2019-05-20 at 8.30.08 PM.png Screen Shot 2019-06-15 at 11.09.33 AM.png Silverlight.dmg URBAN symbiont Urban Lab endosymbiont_2019_pipeline filtered_otu_table1_nocontam.txt high_school_students_in_labs_permission.docx job documents pipeline_general.txt qiime2.rtf sassd.lck software (base) My-Mac:Desktop danaroberts$ cd endosymbiont_2019_pipeline/ (base) My-Mac:endosymbiont_2019_pipeline danaroberts$ source activate qiime2-2019.4 (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path raw_reads/ --input-format FastqGzFormat --output-path qiime2-raw-reads.qza Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 264, in _from_view recorder=recorder) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 59, in make_transformation (self._view_type, other._view_type)) Exception: No transformation from to An unexpected error has occurred: No transformation from to See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path raw_reads/ --input-format SingleLanePerSampleSingleEndFastqDirFmt --output-path qiime2-raw-reads.qza There was a problem importing raw_reads/: Missing one or more files for SingleLanePerSampleSingleEndFastqDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\\.fastq\\.gz' (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path zipped_forward_raw/ --input-format SingleLanePerSampleSingleEndFastqDirFmt --output-path qiime2-raw-reads.qza There was a problem importing zipped_forward_raw/: Missing one or more files for SingleLanePerSampleSingleEndFastqDirFmt: 'MANIFEST' (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample_manifest output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33V2 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 were some problems with the command: (1/3) Invalid value for "--input-path": Path "sample_manifest" does not exist. (2/3) Missing option "--output-path". (3/3) Got unexpected extra arguments (output-path qiime2-raw-reads.qza) (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample_manifest.txt --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33V2 There was a problem importing sample_manifest.txt: sample_manifest.txt is not a(n) SingleEndFastqManifestPhred33V2 file: Filepath on line 1 and column "absolute-filepath" could not be found (Hard drive/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/zipped_forward_raw/G423-035-T4-STR_S35_L001_R1_001.fastq.gz) for sample "CN_BLB_S49". (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample_manifest.txt --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33V2 There was a problem importing sample_manifest.txt: sample_manifest.txt is not a(n) SingleEndFastqManifestPhred33V2 file: Filepath on line 1 and column "absolute-filepath" could not be found (Hard drive/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/zipped_forward_raw/G423-035-T4-STR_S35_L001_R1_001.fastq.gz) for sample "T4_STR_S35". (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample_manifest.txt --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33V2 There was a problem importing sample_manifest.txt: sample_manifest.txt is not a(n) SingleEndFastqManifestPhred33V2 file: Filepath on line 7 and column "absolute-filepath" could not be found (/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/zipped_forward_raw/G423–041-CN-STR_S41_L001_R1_001.fastq.gz) for sample "CN_STR_S41". (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample_manifest.txt --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33V2 There was a problem importing sample_manifest.txt: sample_manifest.txt is not a(n) SingleEndFastqManifestPhred33V2 file: Filepath on line 1 and column "absolute-filepath" could not be found (/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/raw_reads/G423-035-T4-STR_S35_L001_R1_001.fastq) for sample "T4_STR_S35". (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample_manifest.txt --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33V2 There was a problem importing sample_manifest.txt: sample_manifest.txt is not a(n) SingleEndFastqManifestPhred33V2 file: Metadata file must be encoded as UTF-8 or ASCII. The following error occurred when decoding the file: 'utf-8' codec can't decode byte 0xd0 in position 785: invalid continuation byte 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: https://docs.qiime2.org/2019.4/tutorials/metadata/ (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest.tsv --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33V2 There was a problem importing sample-manifest.tsv: sample-manifest.tsv is not a(n) SingleEndFastqManifestPhred33V2 file: Filepath on line 1 and column "absolute-filepath" could not be found (/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/raw_reads/G423-035-T4-STR_S35_L001_R1_001.fastq) for sample "T4_STR_S35". (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest.tsv --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 There was a problem importing sample-manifest.tsv: sample-manifest.tsv is not a(n) SingleEndFastqManifestPhred33 file: Found header on line 1 with the following labels: ['sample-id\tabsolute-filepath'], expected: ['sample-id', 'absolute-filepath', 'direction'] (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path experiment_map.txt --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 There was a problem importing experiment_map.txt: experiment_map.txt is not a(n) SingleEndFastqManifestPhred33 file: Found header on line 2 with the following labels: ['CNBLB\t\t\t1\tCN_BLB_S49.fna\tBLOB\tBACT_16S\tS'], expected: ['sample-id', 'absolute-filepath', 'direction'] (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime metadata tabulate --m-input-file sample-manifest.tsv --o-visualization sample-manifest-metadata.qzv Saved Visualization to: sample-manifest-metadata.qzv (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools view sample-manifest-metadata.qzv Press the 'q' key, Control-C, or Control-D to quit. This view may no longer be accessible or work correctly after quitting. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime metadata tabulate --m-input-file sample-manifest.tsv --o-visualization sample-manifest-metadata.qzv Saved Visualization to: sample-manifest-metadata.qzv (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools view sample-manifest-metadata.qzv Press the 'q' key, Control-C, or Control-D to quit. This view may no longer be accessible or work correctly after quitting. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest-metadata.qzv --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view result = transformation(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 143, in validate view.validate('min') File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/plugin/model/file_format.py", line 24, in validate self._validate_(level) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 193, in _validate_ self._check_n_records(root='', n=None) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 112, in _check_n_records for i, line in file_: File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/encodings/utf_8_sig.py", line 69, in _buffer_decode return codecs.utf_8_decode(input, errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf1 in position 10: invalid continuation byte An unexpected error has occurred: 'utf-8' codec can't decode byte 0xf1 in position 10: invalid continuation byte See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 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 "sample-manifest" does not exist. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest-metadata.qzv --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view result = transformation(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 143, in validate view.validate('min') File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/plugin/model/file_format.py", line 24, in validate self._validate_(level) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 193, in _validate_ self._check_n_records(root='', n=None) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 112, in _check_n_records for i, line in file_: File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/encodings/utf_8_sig.py", line 69, in _buffer_decode return codecs.utf_8_decode(input, errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf1 in position 10: invalid continuation byte An unexpected error has occurred: 'utf-8' codec can't decode byte 0xf1 in position 10: invalid continuation byte See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest-metadata.qzv --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view result = transformation(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 143, in validate view.validate('min') File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/plugin/model/file_format.py", line 24, in validate self._validate_(level) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 193, in _validate_ self._check_n_records(root='', n=None) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 112, in _check_n_records for i, line in file_: File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/encodings/utf_8_sig.py", line 69, in _buffer_decode return codecs.utf_8_decode(input, errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf1 in position 10: invalid continuation byte An unexpected error has occurred: 'utf-8' codec can't decode byte 0xf1 in position 10: invalid continuation byte See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime metadata tabulate --m-input-file sample-manifest.tsv --o-visualization sample-manifest-metadata.qzv Saved Visualization to: sample-manifest-metadata.qzv (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest-metadata.qzv --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view result = transformation(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 143, in validate view.validate('min') File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/plugin/model/file_format.py", line 24, in validate self._validate_(level) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 193, in _validate_ self._check_n_records(root='', n=None) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 112, in _check_n_records for i, line in file_: File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/encodings/utf_8_sig.py", line 69, in _buffer_decode return codecs.utf_8_decode(input, errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf3 in position 12: invalid continuation byte An unexpected error has occurred: 'utf-8' codec can't decode byte 0xf3 in position 12: invalid continuation byte See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime metadata tabulate --m-input-file sample-manifest.tsv --o-visualization sample-manifest-metadata.qzv Saved Visualization to: sample-manifest-metadata.qzv (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest-metadata.qzv --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view result = transformation(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 143, in validate view.validate('min') File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/plugin/model/file_format.py", line 24, in validate self._validate_(level) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 193, in _validate_ self._check_n_records(root='', n=None) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 112, in _check_n_records for i, line in file_: File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/encodings/utf_8_sig.py", line 69, in _buffer_decode return codecs.utf_8_decode(input, errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfa in position 10: invalid start byte An unexpected error has occurred: 'utf-8' codec can't decode byte 0xfa in position 10: invalid start byte See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime metadata --help Usage: qiime metadata [OPTIONS] COMMAND [ARGS]... Description: This QIIME 2 plugin provides functionality for working with and visualizing Metadata. Plugin website: https://github.com/qiime2/q2-metadata Getting user support: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org Options: --version Show the version and exit. --citations Show citations and exit. --help Show this message and exit. Commands: distance-matrix Create a distance matrix from a numeric Metadata column tabulate Interactively explore Metadata in an HTML table (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime metadata tabulate --m-input-file /Users/danaroberts/Documents/emp-single-end-sequences/emp-single-end-sequences.qza --o-visualization emp-single-end-sequences.qzv There was an issue with viewing the artifact /Users/danaroberts/Documents/emp-single-end-sequences/emp-single-end-sequences.qza as QIIME 2 Metadata: Artifact cannot be viewed as QIIME 2 Metadata. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest.txt --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 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 "sample-manifest.txt" does not exist. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sample-manifest --output-path qiime2-raw-reads.qza --input-format SingleEndFastqManifestPhred33 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 "sample-manifest" does not exist. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --source-format SingleEndFastqManifestPhred33 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?) no such option: --source-format (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 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 "/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest" does not exist. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 There was a problem importing /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest: /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest is not a(n) SingleEndFastqManifestPhred33 file: Found header on line 1 with the following labels: ['sample-id\tabsolute-filepath\tdirection'], expected: ['sample-id', 'absolute-filepath', 'direction'] (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 There was a problem importing /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest: /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest is not a(n) SingleEndFastqManifestPhred33 file: Found header on line 1 with the following labels: ['sample-id absolute-filepath direction'], expected: ['sample-id', 'absolute-filepath', 'direction'] (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 There was a problem importing /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest: /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest is not a(n) SingleEndFastqManifestPhred33 file: File referenced on line 2 could not be found (/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/raw_reads/G423-035-T4-STR_S35_L001_R1_001.fastq). (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample_manifest.csv --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 265, in _from_view result = transformation(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 68, in transformation self.validate(view) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 143, in validate view.validate('min') File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/plugin/model/file_format.py", line 24, in validate self._validate_(level) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 193, in _validate_ self._check_n_records(root='', n=None) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_types/per_sample_sequences/_format.py", line 112, in _check_n_records for i, line in file_: File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/encodings/utf_8_sig.py", line 69, in _buffer_decode return codecs.utf_8_decode(input, errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd0 in position 843: invalid continuation byte An unexpected error has occurred: 'utf-8' codec can't decode byte 0xd0 in position 843: invalid continuation byte See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 There was a problem importing /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest: /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest is not a(n) SingleEndFastqManifestPhred33 file: File referenced on line 2 could not be found (/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/raw_reads/G423-035-T4-STR_S35_L001_R1_001.fastq). (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 Traceback (most recent call last): File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 152, in import_data view_type=input_format) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 240, in import_data return cls._from_view(type_, view, view_type, provenance_capture) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 264, in _from_view recorder=recorder) File "/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/core/transform.py", line 59, in make_transformation (self._view_type, other._view_type)) Exception: No transformation from to An unexpected error has occurred: No transformation from to See above for debug info. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest.tsv --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 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 "/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest.tsv" does not exist. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$ qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest.txt --output-path /Users/danaroberts/Desktop/endosymbiont_2019_pipeline/qiime2-reads.qza --input-format SingleEndFastqManifestPhred33 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 "/Users/danaroberts/Desktop/endosymbiont_2019_pipeline/sample-manifest.txt" does not exist. (qiime2-2019.4) My-Mac:endosymbiont_2019_pipeline danaroberts$