Trying download T2T-CHM13

[小林賢子]

Dear Dr.Brian J. Haas

Always thank you.

I want to download T2T-CHM13 to try out FusionInspector with T2T-CHM13, which is said to alleviated the problem of segmental dupliucations, but I cannot download it. 

The error message is as follows.

Do you guess what the problem is?

user@localhost:~/STAR-Fusion$ wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/T2T-CHM13_CTAT_lib_Feb162023.plug-n-play.tar.gz
--2024-11-14 14:08:02--  https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/T2T-CHM13_CTAT_lib_Feb162023.plug-n-play.tar.gz
data.broadinstitute.org (data.broadinstitute.org) をDNSに問いあわせています... 69.173.68.137
data.broadinstitute.org (data.broadinstitute.org)|69.173.68.137|:443 に接続しています... 接続しました。
HTTP による接続要求を送信しました、応答を待っています... 200 OK
長さ: 34769618618 (32G) [application/x-gzip]
`T2T-CHM13_CTAT_lib_Feb162023.plug-n-play.tar.gz.1' に保存中

T2T-CHM13_CTAT_lib_   0%[                    ] 100.08M  2.76MB/s    in 18s    

`T2T-CHM13_CTAT_lib_Feb162023.plug-n-play.tar.gz.1' へ書き込めません(成功です)。

(The underline say that cannot write in `T2T-CHM13_CTAT_lib_Feb162023.plug-n-play.tar.gz.1' (succsess).)

Tetsuko Kobayashi

[Brian Haas]

Hi,

I suggest to try again - note that it can take some time to download, as it's a large file (over 30G).  Hope it comes through.  If you still cannot get it, I can try making it available through a google cloud download and see if that helps.

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Brian Haas]

Hi,

It looks like it all ran well. The KANSL1::ARL17A fusion would normally get filtered out of the star-fusion final results because it's by default going to filter out those fusions that are typically found in normal samples.  

If you include  --no_annotation_filter

 in your STAR-Fusion command, it won't filter out the 'normal' fusion types and these will get further evaluated using FusionInspector.

hope this helps,

Brian

On Sat, Nov 23, 2024 at 10:38 PM 小林賢子 <tkobaya...@gmail.com> wrote:

Dear Dr. Haas,

Thank you very much for the other day.

I could download the T2T-CHM13, and unzipped it using tar command.

Then, I have executed FusionInspector.

I attached the command and outputs in this email.

In the middle, you can see the phrase “* STAR-Fusion complete.  See output: /data/StarFusionOut/star-fusion.fusion_predictions.tsv (or .abridged.tsv version)”. (I highlighted it with yellow.) And that file definitely exists.

However, the outputs continued for a long time after that. Finally, a phrase came and said "Running: touch /data/StarFusionOut/FusionInspector-validate/chckpts_dir/fusion_annotator.ok" (I highlighted it with yellow). Actually the "fusion_annotator.ok" file exists, but is empty.

Q1

I wonder if this FusionInspector session has completed or not?

Q2

The "star-fusion.fusion_predictions.tsv (or .abridged.tsv version)" does not contain KANSL1::ARL17A which was included in the session with GRCh38/hg38 reference.

I'd like to ask you, could you guess why this is?

Sincerely,

Tetsuko Kobayashi

2024年11月14日(木) 23:20 Brian Haas <bh...@broadinstitute.org>:

[Brian Haas]

The system uses checkpoint so it can pick up where earlier jobs left off. If you want to rerun with new parameters, try running in a new working directory so no checkpoints will be reused.

best,

Brian

On Sun, Nov 24, 2024 at 8:24 PM 小林賢子 <tkobaya...@gmail.com> wrote:

Dear Dr. Haas,

Thank you very much for your reply.

I tried it with --no_annotation_filter. The operation was over in an instant. The output file was the same as the previous one. ("OPERATION 1" highlighted in yellow in the attached file.)

Next, I tried it with --no_annotation_filter --denovo_reconstruct. ("OPERATION 2" highlighted in yellow.) Many lines were running, and although there are no errors, it seems that no new files are appearing.

Could you recommend any alternative plans?

Sincerely, 

Tetsuko Kobayashi

2024年11月24日(日) 23:30 Brian Haas <bh...@broadinstitute.org>: