Importing Manifest

Hello everyone,
I am trying to import my manifest file and I keep getting an error. I have my fastq files on a USB drive.

This is the code I am using
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /Volumes/NO\ NAME/data\ collection/Novogene\ downloads\ /Cleandatamanifest.tsv --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2

This is the error I keep getting
There was a problem importing /Volumes/NO NAME/data collection/Novogene downloads /Cleandatamanifest.tsv:

/Volumes/NO NAME/data collection/Novogene downloads /Cleandatamanifest.tsv is not a(n) SingleEndFastqManifestPhred33V2 file:

Filepath on line 1 and column "absolute-filepath" could not be found (/Volumes/NO\ NAME/data\ collection/Novogene\downloads\ /result_X202SC23041434-Z01-F001/00.CleanData/L1B/L1B.effective.fastq.gz) for sample "L1B".

I'm wondering if it is because my data is on my USB drive and not my computer.

This is the first line of my Manifest file (the absolute-filepath line) am I missing anything?
/Volumes/NO\ NAME/data\ collection/Novogene\downloads\ /result_X202SC23041434-Z01-F001/00.CleanData/L1B/L1B.effective.fastq.gz
Thank you in advance!

1 Like

Hi @laurenw31,
Could you send a screenshot of the first five lines of your manifest?

/Volumes/NO\ NAME/data\ collection/Novogene\downloads\ /result_X202SC23041434-Z01-F001/00.CleanData/L1B/L1B.effective.fastq.gz
This is a pretty complicated file path. Have you confirmed that it is correct?
Can you post a screenshot of your cd -ing /Volumes/NO\ NAME/data\ collection/Novogene\downloads\ /result_X202SC23041434-Z01-F001/00.CleanData/L1B/ and ls-ing the directory?

1 Like

when I cd it says no directory found

These are the last 5 lines of my manifest

That is the same error that the importing step gave. It seems like you have to wrong directory listed. You will need to locate where your files are and edit your manifest accordingly. It might help to move these files to your device and not access them from a USB.

Unfortunately, the reason why I asked for the first 5 lines is so that I can make sure the header you have in your manifest is correct. Please provide the first 5 lines of your manifest.

I hope this helps!

1 Like