Hi, please look at my problem. I totally followed the steps on the tutorial page. I think i am in the working directory. What is the problem? and What should I do?
manifest.tsv 100%[=================================================>] 4.53K --.-KB/s in 0s
2023-09-07 14:02:42 (198 MB/s) - ‘manifest.tsv’ saved [4640/4640]
(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ wget \
-O "demultiplexed_seqs.zip"
"https://data.qiime2.org/2023.7/tutorials/pd-mice/demultiplexed_seqs.zip"
--2023-09-07 14:03:35-- https://data.qiime2.org/2023.7/tutorials/pd-mice/demultiplexed_seqs.zip
Resolving data.qiime2.org (data.qiime2.org)... 54.200.1.12, 108.162.193.78, 172.64.33.78, ...
Connecting to data.qiime2.org (data.qiime2.org)|54.200.1.12|:443... connected.
HTTP request sent, awaiting response... 302 FOUND
Location: https://s3-us-west-2.amazonaws.com/qiime2-data/2023.7/tutorials/pd-mice/demultiplexed_seqs.zip [following]
--2023-09-07 14:03:35-- https://s3-us-west-2.amazonaws.com/qiime2-data/2023.7/tutorials/pd-mice/demultiplexed_seqs.zip
Resolving s3-us-west-2.amazonaws.com (s3-us-west-2.amazonaws.com)... 52.92.139.128, 3.5.76.165, 52.218.178.88, ...
Connecting to s3-us-west-2.amazonaws.com (s3-us-west-2.amazonaws.com)|52.92.139.128|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 21508775 (21M) [application/zip]
Saving to: ‘demultiplexed_seqs.zip’
demultiplexed_seqs.zip 100%[=================================================>] 20.51M 6.91MB/s in 3.0s
2023-09-07 14:03:39 (6.91 MB/s) - ‘demultiplexed_seqs.zip’ saved [21508775/21508775]
(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ unzip demultiplexed_seqs.zip
Command 'unzip' not found, but can be installed with:
sudo apt install unzip
(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ head manifest.tsv
sample-id absolute-filepath
recip.220.WT.OB1.D7 $PWD/demultiplexed_seqs/10483.recip.220.WT.OB1.D7_30_L001_R1_001.fastq.gz
recip.290.ASO.OB2.D1 $PWD/demultiplexed_seqs/10483.recip.290.ASO.OB2.D1_27_L001_R1_001.fastq.gz
recip.389.WT.HC2.D21 $PWD/demultiplexed_seqs/10483.recip.389.WT.HC2.D21_1_L001_R1_001.fastq.gz
recip.391.ASO.PD2.D14 $PWD/demultiplexed_seqs/10483.recip.391.ASO.PD2.D14_5_L001_R1_001.fastq.gz
recip.391.ASO.PD2.D21 $PWD/demultiplexed_seqs/10483.recip.391.ASO.PD2.D21_1_L001_R1_001.fastq.gz
recip.391.ASO.PD2.D7 $PWD/demultiplexed_seqs/10483.recip.391.ASO.PD2.D7_15_L001_R1_001.fastq.gz
recip.400.ASO.HC2.D14 $PWD/demultiplexed_seqs/10483.recip.400.ASO.HC2.D14_32_L001_R1_001.fastq.gz
recip.401.ASO.HC2.D7 $PWD/demultiplexed_seqs/10483.recip.401.ASO.HC2.D7_22_L001_R1_001.fastq.gz
recip.403.ASO.PD2.D21 PWD/demultiplexed_seqs/10483.recip.403.ASO.PD2.D21_31_L001_R1_001.fastq.gz
(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial qiime tools import \
--type "SampleData[SequencesWithQuality]"
--input-format SingleEndFastqManifestPhred33V2
--input-path ./manifest.tsv
--output-path ./demux_seqs.qza
There was a problem importing ./manifest.tsv:
manifest.tsv is not a(n) SingleEndFastqManifestPhred33V2 file:
Filepath on line 1 and column "absolute-filepath" could not be found ($PWD/demultiplexed_seqs/10483.recip.220.WT.OB1.D7_30_L001_R1_001.fastq.gz) for sample "recip.220.WT.OB1.D7".
(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ ls
demultiplexed_seqs.zip manifest.tsv metadata.qzv metadata.tsv sample_metadata.tsv
(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ ~