How to download the entire Run from Illumina BaseSpace
Entering edit mode
9 weeks ago
Apex92 ▴ 240

Dear all, I have an account on Illumina basespace and my Run is completed.

Now I want to download the entire run and run bcl2fastq conversion myself. I tried the approaches (my system is mac) mentioned here but I have not been successful to make the download happen.

Everytime I get this error when running executable bs command: ERROR: *** stat /Users/.basespace: no such file or directory ***

Could you please give some input about how I can do it? Thanks

illumina sequencing RNA-seq • 321 views
Entering edit mode
9 weeks ago
Amitm ★ 2.1k

Hi, You must have downloaded the cmdline utility bs. The first step is to authenticate your executable. You probably have done this (?)

$ ./bs auth

When you do that, a unique URL is printed on the cmdline, which you then need to copy into your browser. You are then presented with the sign-in portal of Illumina basespace. Provided that you have had created a log-in already, you need to sign-in. Once you do that, a welcome msg gets printed on the cmdline, saying like "Welcome username".

You are then ready to go. If authentication happened successfully, then under your home directory a file would have been created. It would look like -

$ cat /home/user/.basespace/default.cfg
apiServer   =
accessToken = xxxxxxx54343b3xxxxxa5exxx

Then, you can list out the project thats available in your Ilmn BaseSpace dir. for downloading by doing -

$ ./bs list project
|                        Name                        |    Id     |  TotalSize  |
| 22.10.04_my_prj_xxxxx1_2022-10-04T09_02_03_1xxx137 | 36xxxxxx4 | 36618128088 |

The number under the Id header could then be used to download all fastq under that project. Like -

./bs \
download \
project -i 36xxxxxx4
Entering edit mode

Dear Amitm, thank you for your comment it helped a lot. As you mentioned the problem was with ./bs auth which I had not run before and that was the reason for the error.

I also now get the list as you mentioned but I use the id of the Run to download the entire files (including bcl files) to run the bcl2fastq conversion myself. So for that, I got the Run id by running ./bs list run


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