Raw Sequencing Data Upload Failure

laboratorist · May 26, 2023, 12:49pm

Hi,

I was trying to upload my seq files to try Raw Sequencing Data Platform but I got this error:

and sometimes this error:

Here is a list of files on my PC and the format of the seq files is fq.gz:

D172_S188_L001_R1.zip
D172_S188_L001_R2.zip
D173_S188_L001_R1.zip
D173_S188_L001_R2.zip
D174_S188_L001_R1.zip
D174_S188_L001_R2.zip
D175_S188_L001_R1.zip
D175_S188_L001_R2.zip
D176_S188_L001_R1.zip
D176_S188_L001_R2.zip
D177_S188_L001_R1.zip
D177_S188_L001_R2.zip
D178_S188_L001_R1.zip
D178_S188_L001_R2.zip
D179_S188_L001_R1.zip
D179_S188_L001_R2.zip
D180_S188_L001_R1.zip
D180_S188_L001_R2.zip
D181_S188_L001_R1.zip
D181_S188_L001_R2.zip
D182_S188_L001_R1.zip
D182_S188_L001_R2.zip
D183_S188_L001_R1.zip
D183_S188_L001_R2.zip
D184_S188_L001_R1.zip
D184_S188_L001_R2.zip
D185_S188_L001_R1.zip
D185_S188_L001_R2.zip
D186_S188_L001_R1.zip
D186_S188_L001_R2.zip
D187_S188_L001_R1.zip
D187_S188_L001_R2.zip
D188_S188_L001_R1.zip
D188_S188_L001_R2.zip
D189_S188_L001_R1.zip
D189_S188_L001_R2.zip
D190_S188_L001_R1.zip
D190_S188_L001_R2.zip
D191_S188_L001_R1.zip
D191_S188_L001_R2.zip
D192_S188_L001_R1.zip
D192_S188_L001_R2.zip
D193_S188_L001_R1.zip
D193_S188_L001_R2.zip
D194_S188_L001_R1.zip
D194_S188_L001_R2.zip
D195_S188_L001_R1.zip
D195_S188_L001_R2.zip
D196_S188_L001_R1.zip
D196_S188_L001_R2.zip
D197_S188_L001_R1.zip
D197_S188_L001_R2.zip
D198_S188_L001_R1.zip
D198_S188_L001_R2.zip
D199_S188_L001_R1.zip
D199_S188_L001_R2.zip
D200_S188_L001_R1.zip
D200_S188_L001_R2.zip
D201_S188_L001_R1.zip
D201_S188_L001_R2.zip
D202_S188_L001_R1.zip
D202_S188_L001_R2.zip
D203_S188_L001_R1.zip
D203_S188_L001_R2.zip
D204_S188_L001_R1.zip
D204_S188_L001_R2.zip
D205_S188_L001_R1.zip
D205_S188_L001_R2.zip
D206_S188_L001_R1.zip
D206_S188_L001_R2.zip
D207_S188_L001_R1.zip
D207_S188_L001_R2.zip
D208_S188_L001_R1.zip
D208_S188_L001_R2.zip
D209_S188_L001_R1.zip
D209_S188_L001_R2.zip
D210_S188_L001_R1.zip
D210_S188_L001_R2.zip
D211_S188_L001_R1.zip
D211_S188_L001_R2.zip
D212_S188_L001_R1.zip
D212_S188_L001_R2.zip
D213_S188_L001_R1.zip
D213_S188_L001_R2.zip
D214_S188_L001_R1.zip
D214_S188_L001_R2.zip
D215_S188_L001_R1.zip
D215_S188_L001_R2.zip
D216_S188_L001_R1.zip
D216_S188_L001_R2.zip
D217_S188_L001_R1.zip
D217_S188_L001_R2.zip
D218_S188_L001_R1.zip
D218_S188_L001_R2.zip
D219_S188_L001_R1.zip
D219_S188_L001_R2.zip
D220_S188_L001_R1.zip
D220_S188_L001_R2.zip
D221_S188_L001_R1.zip
D221_S188_L001_R2.zip
D222_S188_L001_R1.zip
D222_S188_L001_R2.zip
D223_S188_L001_R1.zip
D223_S188_L001_R2.zip
D4_S188_L001_R1.zip
D4_S188_L001_R2.zip
metadata.txt

and this is the content of metadata file:

group	type
D173_S188_L001_R1.zip	Pa
D174_S188_L001_R1.zip	Pa
D175_S188_L001_R1.zip	Pa
D176_S188_L001_R1.zip	Pa
D177_S188_L001_R1.zip	Pa
D178_S188_L001_R1.zip	Pa
D179_S188_L001_R1.zip	Pa
D180_S188_L001_R1.zip	Pa
D181_S188_L001_R1.zip	Pa
D182_S188_L001_R1.zip	Pa
D183_S188_L001_R1.zip	Pa
D184_S188_L001_R1.zip	Pa
D185_S188_L001_R1.zip	Pa
D186_S188_L001_R1.zip	Pa
D187_S188_L001_R1.zip	Pa
D188_S188_L001_R1.zip	Pa
D189_S188_L001_R1.zip	Pa
D190_S188_L001_R1.zip	Pa
D191_S188_L001_R1.zip	Pa
D192_S188_L001_R1.zip	Pa
D193_S188_L001_R1.zip	Pa
D194_S188_L001_R1.zip	Pa
D195_S188_L001_R1.zip	Pa
D196_S188_L001_R1.zip	Pa
D197_S188_L001_R1.zip	Pa
D218_S188_L001_R1.zip	BCC
D219_S188_L001_R1.zip	BCC
D220_S188_L001_R1.zip	BCC
D221_S188_L001_R1.zip	BCC
D222_S188_L001_R1.zip	BCC
D223_S188_L001_R1.zip	BCC
D224_S188_L001_R1.zip	BCC
D225_S188_L001_R1.zip	BCC
D226_S188_L001_R1.zip	BCC
D227_S188_L001_R1.zip	BCC
D228_S188_L001_R1.zip	BCC
D229_S188_L001_R1.zip	BCC
D230_S188_L001_R1.zip	BCC
D217_S188_L001_R1.zip	Pa
D198_S188_L001_R1.zip	Pa
D199_S188_L001_R1.zip	Pa
D200_S188_L001_R1.zip	Pa
D201_S188_L001_R1.zip	Pa
D202_S188_L001_R1.zip	Pa
D203_S188_L001_R1.zip	Pa
D204_S188_L001_R1.zip	Pa
D205_S188_L001_R1.zip	Pa
D206_S188_L001_R1.zip	Pa
D207_S188_L001_R1.zip	Pa
D208_S188_L001_R1.zip	Pa
D209_S188_L001_R1.zip	Pa
D210_S188_L001_R1.zip	Pa
D211_S188_L001_R1.zip	Pa
D212_S188_L001_R1.zip	Pa
D213_S188_L001_R1.zip	Pa
D214_S188_L001_R1.zip	Pa
D215_S188_L001_R1.zip	Pa
D216_S188_L001_R1.zip	Pa
D172_S188_L001_R1.zip	mock
D4_S188_L001_R1.zip	blank
D173_S188_L001_R2.zip	Pa
D174_S188_L001_R2.zip	Pa
D175_S188_L001_R2.zip	Pa
D176_S188_L001_R2.zip	Pa
D177_S188_L001_R2.zip	Pa
D178_S188_L001_R2.zip	Pa
D179_S188_L001_R2.zip	Pa
D180_S188_L001_R2.zip	Pa
D181_S188_L001_R2.zip	Pa
D182_S188_L001_R2.zip	Pa
D183_S188_L001_R2.zip	Pa
D184_S188_L001_R2.zip	Pa
D185_S188_L001_R2.zip	Pa
D186_S188_L001_R2.zip	Pa
D187_S188_L001_R2.zip	Pa
D188_S188_L001_R2.zip	Pa
D189_S188_L001_R2.zip	Pa
D190_S188_L001_R2.zip	Pa
D191_S188_L001_R2.zip	Pa
D192_S188_L001_R2.zip	Pa
D193_S188_L001_R2.zip	Pa
D194_S188_L001_R2.zip	Pa
D195_S188_L001_R2.zip	Pa
D196_S188_L001_R2.zip	Pa
D197_S188_L001_R2.zip	Pa
D218_S188_L001_R2.zip	BCC
D219_S188_L001_R2.zip	BCC
D220_S188_L001_R2.zip	BCC
D221_S188_L001_R2.zip	BCC
D222_S188_L001_R2.zip	BCC
D223_S188_L001_R2.zip	BCC
D224_S188_L001_R2.zip	BCC
D225_S188_L001_R2.zip	BCC
D226_S188_L001_R2.zip	BCC
D227_S188_L001_R2.zip	BCC
D228_S188_L001_R2.zip	BCC
D229_S188_L001_R2.zip	BCC
D230_S188_L001_R2.zip	BCC
D217_S188_L001_R2.zip	Pa
D198_S188_L001_R2.zip	Pa
D199_S188_L001_R2.zip	Pa
D200_S188_L001_R2.zip	Pa
D201_S188_L001_R2.zip	Pa
D202_S188_L001_R2.zip	Pa
D203_S188_L001_R2.zip	Pa
D204_S188_L001_R2.zip	Pa
D205_S188_L001_R2.zip	Pa
D206_S188_L001_R2.zip	Pa
D207_S188_L001_R2.zip	Pa
D208_S188_L001_R2.zip	Pa
D209_S188_L001_R2.zip	Pa
D210_S188_L001_R2.zip	Pa
D211_S188_L001_R2.zip	Pa
D212_S188_L001_R2.zip	Pa
D213_S188_L001_R2.zip	Pa
D214_S188_L001_R2.zip	Pa
D215_S188_L001_R2.zip	Pa
D216_S188_L001_R2.zip	Pa
D172_S188_L001_R2.zip	mock
D4_S188_L001_R2.zip	blank

I don’t understand what is the problem and how to troubleshoot it.

Any help is highly appreciated!

Regards,
Abdul

Yao · May 27, 2023, 5:46pm

Hello,
It seems caused by the format of the metadata according to the error message. Could you please share the metadata file as well as several zip file as an example for further trouble shooting?

laboratorist · May 27, 2023, 5:56pm

Hi @Yao ,

Thank you for your reply,

Here is the metadata file:

metadata.txt (3.1 KB)

I cannt upload .zip file (it is not supported here)!

Many thanks in advance,

Yao · May 30, 2023, 2:29am

Hello,
I have check the metafile and it seems all right. But I cannot open the link you shared with me. Could you please send me the sequence data by email(yao.lu5@mail.mcgill.ca) if it’s necessary?

Yao · May 31, 2023, 1:48am

Hello,
I have test your example data and it works well as shown below：

Could you please try again and let me know if you have additional reminder information to figure out the issue?
Please make sure all the file names are matched with the metadata.

laboratorist · June 1, 2023, 11:15pm

Many thanks @Yao for your time and try.

I still have the same issue - i get this error: please end your file with with “R1.fastq”!

Many thanks,
Abdul

dvauzour · June 2, 2023, 9:09am

Hi
I exactly have the same issue and this has been for a while. Also analysis stops at 8% without going any further.
best wishes

David

laboratorist · June 2, 2023, 11:25am

Hi @dvauzour and @Yao,

I tried google chrome of few files and it seems work OK so far.

I will test it with all samples and see if things go well

regards,
Abdul

laboratorist · June 5, 2023, 4:30pm

Hi @Yao,

after successfuly uploaded seq files, it kept asking me this confirmation question:

I click on yes, and doing its magic in the background and bringing the Yes icon again. this happens more than 5 times now!

Any help in appreciated!

Cheers,
Abdul

laboratorist · June 17, 2023, 9:13pm

Any help is appreciated!

Cheers,
Abdul

Yao · June 18, 2023, 3:06am

Hello, we have just update our website. You can have another try.
If you want to process more than 100 files, you can either using our R package or upload twice to the website.
Hope this helps!

MMORI · June 18, 2023, 2:31pm

Hello,

I had the same problem. Actually I’m trying to load Nanopore data (possible?). But I had the window: we noticed your data are single-ended, right? I kept on doing yes for 73 times (I thought was for each file) but NO…

Thank you for any help
Marcella

laboratorist · June 18, 2023, 3:51pm

Thank you @Yao for your reply,

I just tried and still the issue persists!

regards,
Abdul

Yao · June 19, 2023, 3:36pm

Hello, this is a little bit confusing. Because I use the example you provided:

This works well and took 1 second to pass that step as shown:

Can you please simply try this example data to help figure out where the error comes from.

Hope we will make it soon

laboratorist · June 19, 2023, 5:59pm

Hi @Yao,

It works for the 4 samples, but does not for the batch of ~ 60 samples!

Cheers, Abdul

jeff.xia · June 24, 2023, 12:00pm

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