csv is not a(n) PairedEndFastqManifestPhred33 file:

[razz1618]

Hi, i am new to qiime. While importing data I got two errors:
"There was a problem importing man.csv:

man.csv is not a(n) PairedEndFastqManifestPhred33 file:

File referenced on line 2 could not be found (/raw_data/A1_R1.fq.gz)."

My manifest file is in .csv format and looks like this
sample-id,absolute-filepath,direction
A1,/raw_data/A1_R1.fq.gz,forward
A1,/raw_data/A1_R2.fq.gz,reverse
A2,/raw_data/A2_R1.fq.gz,forward
A2,/raw_data/A2_R2.fq.gz,reverse
B1,/raw_data/B1_R1.fq.gz,forward
B1,/raw_data/B1_R2.fq.gz,reverse
B2,/raw_data/B2_R1.fq.gz,forward
B2,/raw_data/B2_R2.fq.gz,reverse
C1,/raw_data/C1_R1.fq.gz,forward
C1,/raw_data/C1_R2.fq.gz,reverse
C2,/raw_data/C2_R1.fq.gz,forward
C2,/raw_data/C2_R2.fq.gz,reverse
D1,/raw_data/D1_R1.fq.gz,forward
D1,/raw_data/D1_R2.fq.gz,reverse
D2,/raw_data/D2_R1.fq.gz,forward
D2,/raw_data/D2_R2.fq.gz,reverse
E1,/raw_data/E1_R1.fq.gz,forward
E1,/raw_data/E1_R2.fq.gz,reverse
E2,/raw_data/E2_R1.fq.gz,forward
E2,/raw_data/E2_R2.fq.gz,reverse
F1,/raw_data/F1_R1.fq.gz,forward
F1,/raw_data/F1_R2.fq.gz,reverse
F2,/raw_data/F2_R1.fq.gz,forward
F2,/raw_data/F2_R2.fq.gz,reverse
G1,/raw_data/G1_R1.fq.gz,forward
G1,/raw_data/G1_R2.fq.gz,reverse
G2,/raw_data/G2_R1.fq.gz,forward
G2,/raw_data/G2_R2.fq.gz,reverse

The command I used is:

qiime tools import **

–type ‘SampleData[PairedEndSequencesWithQuality]’ **

–input-path man.csv **

–output-path raw_data//reads.qza \

–input-format PairedEndFastqManifestPhred33

I’m in the main folder containing sub-folders “raw_data” and “reads-qza”

Here is the link for the fatq files and manifest file https://drive.google.com/file/d/1X6HhZmS5f3tgoTIaQYMR2R2StsEOZMMy/view?usp=sharing

Kindly, help me out. Thanks

[ChrisKeefe]

Welcome to the forum, @razz1618!
Thanks for the detailed post. I suspect this is the key part of your error:

@razz1618

File referenced on line 2 could not be found (/raw_data/A1_R1.fq.gz)."

Almost everything in QIIME 2 can handle relative file paths, but manifest files must use absolute file paths. I could be wrong, but it looks like your file paths are malformed.

/ is a specific directory in linux/macos. If you start a file path with /, that means everything else in your path is nested directly under the root directory. E.g. if I enter /mydirectory/myfile.txt, I am telling the computer to look for mydirectory in /, and not in whatever folder I happen to be in when I run the command.

Running the pwd command from the directory your files are in should tell you what the absolute filepath to that directory is.

If you're not familiar with how file relative and absolute paths work in unix-like systems, you should probably do a little reading. I still make incorrect file path errors all the time, and understanding how they work will help a ton. I'm sure there are far better resources out there, but here's a quick start and the wikipedia article.

[razz1618]

Thanks, I had tried with $pwd before (following standard qiime2 SOP) and it showed similar error so I changed to " /mydirectory/..... But the actual problem was my some zipped fastq files had “.fq.gz” and a few had ".fastq.gz extension. Earlier I missed to notice it but now rectified. Thanks.

[ChrisKeefe]

Glad you figured it out! Try as I might, incorrect file paths bite me all the time.

[razz1618]

yes, finally all running well. thanks