trinityctat/ctatfusion Docker image does not exist

[meishiue]

Hello,
I tried to follow this tutorial but got an error message in "docker pull trinityctat/ctatfusion".
trinityctat/ctatfusion Docker image does not exist.

I have pulled jfx319/ctatfusion but it does not come with prep_genome_lib.pl

Could you tell me if any Docker image replace trinityctat/ctatfusion?

Thank you for your help,

[brianjohnhaas]

Hi, Can you point me to the tutorial that you're using? The current docker is pulled like so: docker pull trinityctat/starfusion

…

On Sun, Oct 30, 2022 at 5:12 PM meishiue ***@***.***> wrote: Hello, I tried to follow this tutorial but got an error message in "docker pull trinityctat/ctatfusion". trinityctat/ctatfusion Docker image does not exist. I have pulled jfx319/ctatfusion but it does not come with prep_genome_lib.pl Could you tell me if any Docker image replace trinityctat/ctatfusion? Thank you for your help, — Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXYZUXAQX44EDVQT3WDWF3JDFANCNFSM6AAAAAARSQIFHI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[meishiue]

Hello Brian, Thank you very much for your quick response. The tutorial that I am using is : https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/wiki I have pulled the mentioned docker image (trinityctat/starfusion) and perform git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git > to have Tutorial Data git clone --recursive https://github.com/STAR-Fusion/STAR-Fusion.git > to have prep_genome_lib.pl for Preparing a CTAT Genome Lib Since my PC is not powerful enough, I tried to use the small Tutorial Data (from https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/wiki) to make STAR-fusion work. Genome data: minigenome.fa : small genome sequence consisting of ~750 genes. minigenome.gtf : transcript structure annotations for these genes. RNA-Seq data: rnaseq_1.fastq.gz : RNA-Seq read 1 data ('left' read) rnaseq_2.fastq.gz : RNA-Seq read 2 data ('right' read) Meta data: CTAT_HumanFusionLib.mini.dat.gz : a small fusion annotation library Unfortunately, it still did not work. Firstly, I performed Preparing a CTAT Genome Lib using the following code : docker run --rm -it -v ${pwd}:/data trinityctat/starfusion:latest bash cd /data ctat-genome-lib-builder/prep_genome_lib.pl \ --genome_fa minigenome.fa \ --gtf minigenome.gtf \ --dfam_db human \ it seems to block in the step without ending * Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile homo_sapiens_dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4 Could you help me to deal with this problem? Here is the screen capture : [image: image.png] Thank you very much for your help. Mei-Shiue

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On Mon, Oct 31, 2022 at 7:07 PM Brian Haas ***@***.***> wrote: Hi, Can you point me to the tutorial that you're using? The current docker is pulled like so: docker pull trinityctat/starfusion On Sun, Oct 30, 2022 at 5:12 PM meishiue ***@***.***> wrote: > Hello, > I tried to follow this tutorial but got an error message in "docker pull > trinityctat/ctatfusion". > trinityctat/ctatfusion Docker image does not exist. > > I have pulled jfx319/ctatfusion but it does not come with > prep_genome_lib.pl > > Could you tell me if any Docker image replace trinityctat/ctatfusion? > > Thank you for your help, > > — > Reply to this email directly, view it on GitHub > <#6>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABZRKXYZUXAQX44EDVQT3WDWF3JDFANCNFSM6AAAAAARSQIFHI > > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIMMXQ4NJ6DJ4SYUO5J2GH3WGADEPANCNFSM6AAAAAARSQIFHI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Mei-Shiue KUO 8 Run Eugène Chevreul 33160 Saint-Médard-en-Jalles France +33 (0)676104827

[brianjohnhaas]

hi, I'll take a look at this later today and see if I can get it to run. If you could retry adding your screenshot above, that would be helpful. It didn't come through earlier. best, ~b

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On Wed, Nov 2, 2022 at 5:53 PM meishiue ***@***.***> wrote: Hello Brian, Thank you very much for your quick response. The tutorial that I am using is : https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/wiki I have pulled the mentioned docker image (trinityctat/starfusion) and perform git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git > to have Tutorial Data git clone --recursive https://github.com/STAR-Fusion/STAR-Fusion.git > to have prep_genome_lib.pl for Preparing a CTAT Genome Lib Since my PC is not powerful enough, I tried to use the small Tutorial Data (from https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/wiki) to make STAR-fusion work. Genome data: minigenome.fa : small genome sequence consisting of ~750 genes. minigenome.gtf : transcript structure annotations for these genes. RNA-Seq data: rnaseq_1.fastq.gz : RNA-Seq read 1 data ('left' read) rnaseq_2.fastq.gz : RNA-Seq read 2 data ('right' read) Meta data: CTAT_HumanFusionLib.mini.dat.gz : a small fusion annotation library Unfortunately, it still did not work. Firstly, I performed Preparing a CTAT Genome Lib using the following code : docker run --rm -it -v ${pwd}:/data trinityctat/starfusion:latest bash cd /data ctat-genome-lib-builder/prep_genome_lib.pl \ --genome_fa minigenome.fa \ --gtf minigenome.gtf \ --dfam_db human \ it seems to block in the step without ending * Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile homo_sapiens_dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4 Could you help me to deal with this problem? Here is the screen capture : [image: image.png] Thank you very much for your help. Mei-Shiue On Mon, Oct 31, 2022 at 7:07 PM Brian Haas ***@***.***> wrote: > Hi, > > Can you point me to the tutorial that you're using? > > The current docker is pulled like so: > docker pull trinityctat/starfusion > > > > On Sun, Oct 30, 2022 at 5:12 PM meishiue ***@***.***> wrote: > > > Hello, > > I tried to follow this tutorial but got an error message in "docker pull > > trinityctat/ctatfusion". > > trinityctat/ctatfusion Docker image does not exist. > > > > I have pulled jfx319/ctatfusion but it does not come with > > prep_genome_lib.pl > > > > Could you tell me if any Docker image replace trinityctat/ctatfusion? > > > > Thank you for your help, > > > > — > > Reply to this email directly, view it on GitHub > > <#6>, or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ABZRKXYZUXAQX44EDVQT3WDWF3JDFANCNFSM6AAAAAARSQIFHI > > > > . > > You are receiving this because you are subscribed to this thread.Message > > ID: ***@***.***> > > > > > -- > -- > Brian J. Haas > The Broad Institute > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > > — > Reply to this email directly, view it on GitHub > < #6 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AIMMXQ4NJ6DJ4SYUO5J2GH3WGADEPANCNFSM6AAAAAARSQIFHI > > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- Mei-Shiue KUO 8 Run Eugène Chevreul 33160 Saint-Médard-en-Jalles France +33 (0)676104827 — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX6C2PO3K4YREKWZQ5DWGLPHNANCNFSM6AAAAAARSQIFHI> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[meishiue]

Hi,
the screen capture is not attached correctly, sorry.

[brianjohnhaas]

Thanks! It might just be that the dfam step takes a long time. Years ago, we had a different process that was faster. I'll look into it, though, and see what the issue is. more later, ~b

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On Thu, Nov 3, 2022 at 9:24 AM meishiue ***@***.***> wrote: Hi, the screen capture is not attached correctly, sorry. [image: Screenshot 2022-11-03 142248] <https://user-images.githubusercontent.com/35179459/199732328-e958f28b-73e3-4b48-be59-8587bfbc3bd9.png> — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX7THXPIY4T2POB3LJLWGO4KTANCNFSM6AAAAAARSQIFHI> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[brianjohnhaas]

I've now updated the tutorial: https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/wiki so it should work with the current docker. Note, the dfam step does take a while (could be near an hour). I've updated the docker command itself so it mounts the /tmp directory, which is something that wasn't happening earlier and was probably a reason for the dfam step taking even longer. Some of the other tutorial commands are updated too so they match the current use. Let me know if it gives you any more trouble. best, ~b

[meishiue]

Thank you very much for updating the indicated tutorial.

I have tried to work with the updated docker command yesterday and it is still at the dfam step ( around 8 hours later).
I will let you know if this dfam step ends one day.

Otherwise, I am downloading the plug-n-play version of CTAT Genome Lib GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz. Hope this download could end without any trouble.

Could you confirm me that this GRCh38_gencode_v37_CTAT_lib is compatible with the tutorial data?

Thank you again for your helps and suggestions.

[brianjohnhaas]

Yes, it should be compatible with the tutorial. Let me know if that works for you. I think I'll update the tutorial to use it anyway, because the new build-from-scratch step is overly cumbersome now (but worth the effort for routine use). best, ~b

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On Fri, Nov 4, 2022 at 2:08 AM meishiue ***@***.***> wrote: Thank you very much for updating the indicated tutorial. I have tried to work with the updated docker command yesterday and it is still at the dfam step ( around 8 hours later). I will let you know if this dfam step ends one day. Otherwise, I am downloading the plug-n-play version of CTAT Genome Lib GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz <https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz>. Hope this download could end without any trouble. Could you confirm me that this GRCh38_gencode_v37_CTAT_lib is compatible with the tutorial data? Thank you again for your helps and suggestions. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXZKZQJGBWJ476LXSD3WGSR4TANCNFSM6AAAAAARSQIFHI> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[meishiue]

Hello,

I'd like you know that the "Preparing a CTAT Genome Lib" step ends with success after 4 days of running with updated docker command line.

I can finally try to use STAR-fusion to predict Fusions.

Thank you again for your helps.

[brianjohnhaas]

ouch... 4 days! that's pretty awful. Did you try running the tutorial with the plug-n-play genome lib we provide for regular use?

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On Mon, Nov 7, 2022 at 5:03 PM meishiue ***@***.***> wrote: Hello, I'd like you know that the "Preparing a CTAT Genome Lib" step ends with success after 4 days of running with updated docker command line. I can finally try to use STAR-fusion to predict Fusions. Thank you again for your helps. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXYT6BEHKXHWW22WW33WHF4CFANCNFSM6AAAAAARSQIFHI> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[meishiue]

Yes, I tried to run the tutorial with plug-n-play genome lib but I don't think it works.

Maybe I did something wrong.

1. I putted the [GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz] in the same directory of STAR-Fusion (should I put in a specified directory ?)
2. I launched docker run with following command lines :
   docker run --rm -it -v ${pwd}:/data trinityctat/starfusion:latest bash
   cd /data/
   STAR-Fusion
   --left_fq rnaseq_1.fastq.gz
   --right_fq rnaseq_2.fastq.gz
   --output_dir star_fusion_outdir

I saw STAR-Fusion printing on the screen but I do not have the expected star_fusion_outdir

Here is the capture of my screen :

[brianjohnhaas]

You can try using this genome lib instead of the one you built for the tutorial. Just put it in the same directory as your input reads, untar it, and you'll find the ctat_genome_lib within it. Then set --genome_lib_dir to that instead of the other one. Let me know if that needs more explanation. best, ~b

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On Mon, Nov 7, 2022 at 5:47 PM meishiue ***@***.***> wrote: Yes, I tried to run the tutorial with plug-n-play genome lib but I don't think it works. Maybe I did something wrong. 1. I putted the [GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz] in the same directory of STAR-Fusion (should I put in a specified directory ?) 2. I launched docker run with following command lines : docker run --rm -it -v ${pwd}:/data trinityctat/starfusion:latest bash cd /data/ STAR-Fusion --left_fq rnaseq_1.fastq.gz --right_fq rnaseq_2.fastq.gz --output_dir star_fusion_outdir I saw STAR-Fusion on the screen but I d [image: Screenshot 2022-11-07 234625] <https://user-images.githubusercontent.com/35179459/200431595-40e80739-e708-4bcf-b476-d41f0c5c144f.png> o nt have the expected star_fusion_outdir Here is the capture of my screen : [image: Screenshot 2022-11-07 234625] <https://user-images.githubusercontent.com/35179459/200431658-b8cc0bbc-aea8-460b-84d9-17fb6951eb3e.png> — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3X66AAC5WKY4RUPHLWHGBJLANCNFSM6AAAAAARSQIFHI> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[meishiue]

I tried to run STAR-Fusion using the plug-n-play genome lib s you mentioned but it stopped due to insufficient RAM.

i think it will work if I have enough RAM.

[brianjohnhaas]

oh, right. Sounds good. Definitely needs a lot more ram here. I guess I could make a small tutorial-based ctat genome lib available for smaller RAM requirements.

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On Tue, Nov 8, 2022 at 1:01 PM meishiue ***@***.***> wrote: I tried to run STAR-Fusion using the plug-n-play genome lib s you mentioned but it stopped due to insufficient RAM. i think it will work if I have enough RAM. [image: Screenshot 2022-11-08 185509] <https://user-images.githubusercontent.com/35179459/200640976-a6887286-2e2a-4ad4-8c76-b2db27913f10.png> — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX7LNWQ7L36ZD6DJ2HLWHKIQHANCNFSM6AAAAAARSQIFHI> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>