Importing files after installing qiime2-2020.6

[Arun04 (Arutchelvan Rajamanikam)]

I am having issues with importing my files after installing qiime2-2020.6. i chose paired end demultiplexed fastq.

Below is the error message:

There was a problem importing sample-manifest-crc.csv:

sample-manifest-crc.csv is not a(n) PairedEndFastqManifestPhred33 file:

File referenced on line 2 could not be found (/Users/User/TRGS/Samples/CRC/AR-CR001_S1_L001_R1_001.fastq).

Attaching my manifest file here:
sample-manifest-crc.csv (12.1 KB)

please help.

[jwdebelius (Justine Debelius)]

Hi @Arun04,

The error says your path is incorrect. I see that yo u have \User\ listed twice in the path, and my suspecion is that it's a mistake. I would try removing that first \User and see if it fixes the problem.

File referenced on line 2 could not be found (/Users/User/TRGS/Samples/CRC/AR-CR001_S1_L001_R1_001.fastq).

Best,
Justine

[Arun04 (Arutchelvan Rajamanikam)]

Dear @jwdebelius,

Thanks a lot for the reply.

That is where I have stored my sequences. It is in a subfolder ‘User’ which is inside the folder ‘Users’. I don’t think it could the problem as I just copied the pathname into the sample manifest.

Please help.

Regards,
ARR

[jwdebelius (Justine Debelius)]

Hi @Arun04,

I would then go to that folder

cd /Users/User/TRGS/Samples/CRC/

and make sure the sample file is present

ls

Best,
Justine

[Arun04 (Arutchelvan Rajamanikam)]

Hi @jwdebelius,

I tried your suggestion and the file is present( as attached)

. I have a few fastq files(from different samples) in one folder, do you think that is causing the problem?

[jwdebelius (Justine Debelius)]

Hi @Arun04,

The error says the file isn’t there, so you need to make sure it’s present and the folder is connected. You could try ls | grep AR-CR001_S1_L001_R1_001.fastq to see if you can find the file.

Best,
Justine

[Arun04 (Arutchelvan Rajamanikam)]

@jwdebelius

ls | grep AR-CR001_S1_L001_R1_001.fastq

Dear @jwdebelius,

I tried as you suggested. The error now is :

File referenced on line 6 could not be found (/Users/User/TRGS/Samples/CRC/AR-CT003_S3_L001_R1_001.fastq).

I realize that when I use "ls | AR-CT003_S3_L001_R1_001.fastq", nothing is returned. I have attached the screenshot for your reference.

Please help.

[jwdebelius (Justine Debelius)]

Hi @Arun04,

We just talked about what the error means. What’s the problem the manifest is warning you about?
What does the output of the ls command tell you? (grep lets you search for specific things so rather than getting. everything from ls, you’re just getting a specific result).
Why do you think I recommended these steps?

Best,
Justine

[Arun04 (Arutchelvan Rajamanikam)]

Hi @jwdebelius,

It seemed that the file was corrupted. Replacing the file managed to solve the issue. Thanks a lot for your support and advises.

Thank you.

Regards.

Arun