I honestly have no idea why this doesn’t work, but I keep getting an error when trying to import my single ended, non-EMP or Cassava .fastq files by running this command:
qiime tools import
–input-format SingleEndFastqManifestPhred33V2 \
The error that is given is:
There was a problem importing seqs.tsv:
seqs.tsv is not a(n) SingleEndFastqManifestPhred33V2 file:
Filepath on line 1 and column “absolute-filepath” could not be found (./Desktop/Hines/FASTQ_Seqs/HCl-1_R1.fastq) for sample “HCl-1”.
When I try to use the --verbose command, I get this error:
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.
–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.
–output-path ARTIFACT Path where output artifact should be written.
–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 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: --verbose
I am including my manifest file that has been cleared by Keemei as well as a handful of my sequence files (.fastq).
seqs.tsv (21.6 KB)
HCl-1_R1.fastq (688 Bytes) HCl-2_R1.fastq (690 Bytes) HCl-3_R1.fastq (690 Bytes) HCl-4_R1.fastq (690 Bytes) HCl-5_R1.fastq (688 Bytes) HCl-6_R1.fastq (690 Bytes) HCl-7_R1.fastq (692 Bytes) HCl-9_R1.fastq (689 Bytes) HCl-10_R1.fastq (693 Bytes)
These sequences are from Sanger sequencing, so I know from this link that I have a Phred33 offset.
Why isn’t this a SingleEndManifestPred33V2 file?? Why can’t these files be found? I know the directory string is correct. Should I type out every single bit of that file path (e.g. MacHD/Users/Desktop/Hines/…)?
I’m running out of time & getting frustrated. Any help is greatly appreciated.