mutation-lib supplement for GRCm39

[cachedpotato]

Hello,

I've been testing CTAT-mutations on various datasets and it's been working pretty well, but I was wondering if this can be made compatible with mouse samples as well.
To my understanding I need a mutations-lib supplement for this to work, and it seems like there isn't one for GRCm39 (Understandably so, as this was made primarily for variant detection in human genome, not mouse). Is there any chance you have the files, or if I have to make it myself, could you give me any insight on where to start?

Thanks!

[brianjohnhaas]

Glad to hear it's working well for human. It might be possible to have it run in the most basic way on mouse, just generating a vcf without all the various annotations. I could look into that if it's of interest.

…

On Wed, Apr 10, 2024 at 8:24 PM cachedpotato ***@***.***> wrote: Hello, I've been testing CTAT-mutations on various datasets and it's been working pretty well, but I was wondering if this can be made compatible with mouse samples as well. To my understanding I need a mutations-lib supplement for this to work, and it seems like there isn't one for GRCm39 (Understandably so, as this was made primarily for variant detection in human genome, not mouse). Is there any chance you have the files, or if I have to make it myself, could you give me any insight on where to start? Thanks! — Reply to this email directly, view it on GitHub <#134>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXYMHWG7U7LXJ6IBZKDY4XJ3PAVCNFSM6AAAAABGBLEMQCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTMNRUGEZDOMY> . 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>

[cachedpotato]

Thank you for the reply! I do have a vcf file with me, I'll check if it works.
I'll close the issue for now, and re-open it if I run into some problems.

Again, thank you for your help!

[cachedpotato]

Hello,

Unfortunately I'm having problems with using GRCm39 data.
I'm trying to run CTAT-mutations with Docker, and I'm getting this error message:

Cannot find properties.json file in /ctat_genome_lib_dir/ctat_mutation_lib

the way I run the docker container is through a shell file like so:

#!/bin/bash

DATA_FOLDER=/home/user/CTAT-mutations/fastqc_trimmed_results_39
CTAT_GENOME_LIB=/home/user/CTAT-mutations/ctat_genome_lib_build_dir
docker run --rm -v ${DATA_FOLDER}:${DATA_FOLDER} -v /tmp:/tmp \
         -v ${CTAT_GENOME_LIB}:/ctat_genome_lib_dir:ro \
         trinityctat/ctat_mutations \
        /usr/local/src/ctat-mutations/ctat_mutations \
        --left ${DATA_FOLDER}/reads_1.fastq.gz \
        --right ${DATA_FOLDER}/reads_2.fastq.gz \
        --sample_id mm39 \
        --output ${DATA_FOLDER}/ctat_mutations_outdir \
        --cpu 4 \
        --genome_lib_dir /ctat_genome_lib_dir

while I did not have any problems generating mutations_lib directory, it did not create properties.json file as mentioned in the error message.

I also tried changing --genome_lib_dir line to genome_lib_dir /home/user/CTAT-mutations/ctat_genome_lib_build_dir but that gives me this message:

Missing path to CTAT_GENOME_LIB in $CTAT_GENOME_LIB.

Is there anything else I should do to create properties.json?

Thanks!

[brianjohnhaas]

Hi, In your ctat_mutations_lib/ directory, create a file 'properties.json' that has contents like this: { "Genome_version":"hg38" } But has the mouse genome info. Specifically, this is used for snpEff, so put here whatever the value is that would get propagated to the snpEff command: java -Xmx3500m -jar ~{plugins_path}/snpEff.jar \ -nostats -noLof -no-downstream -no-upstream -noLog \ ~{genome_version} Best of luck, Brian

On Wed, Apr 17, 2024 at 9:25 PM cachedpotato ***@***.***> wrote: Hello, Unfortunately I'm having problems with using GRCm39 data. I'm trying to run CTAT-mutations with Docker, and I'm getting this error

message:

Cannot find properties.json file in /ctat_genome_lib_dir/ctat_mutation_lib the way I run the docker container is through a shell file like so: #!/bin/bash DATA_FOLDER=/home/user/CTAT-mutations/fastqc_trimmed_results_39 CTAT_GENOME_LIB=/home/user/CTAT-mutations/ctat_genome_lib_build_dir docker run --rm -v ${DATA_FOLDER}:${DATA_FOLDER} -v /tmp:/tmp \ -v ${CTAT_GENOME_LIB}:/ctat_genome_lib_dir:ro \ trinityctat/ctat_mutations \ /usr/local/src/ctat-mutations/ctat_mutations \ --left ${DATA_FOLDER}/reads_1.fastq.gz \ --right ${DATA_FOLDER}/reads_2.fastq.gz \ --sample_id mm39 \ --output ${DATA_FOLDER}/ctat_mutations_outdir \ --cpu 4 \ --genome_lib_dir /ctat_genome_lib_dir while I did not have any problems generating mutations_lib directory, it

did not create properties.json file as mentioned in the error message.

I also tried changing --genome_lib_dir line to genome_lib_dir

/home/user/CTAT-mutations/ctat_genome_lib_build_dir but that gives me this message:

Missing path to CTAT_GENOME_LIB in $CTAT_GENOME_LIB. Is there anything else I should do to create properties.json? Thanks! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID:

***@***.***>

…

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

[cachedpotato]

Thank you for your help! I greatly appreciate it.

I'm still encountering problems unfortunately. First, here's the log file I made.
log.txt
It's quite long, but I'll try my best to summarize.
At some point I started getting a bunch of this message:

... Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions.

then I got some error related to SplitIntervals:

Job ctat_mutations.SplitIntervals:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.

After which GATK failed to run and the Workflow transitioned to failed state.

I'm not a competent coder, nor do I know anything about .wdl files, but searching through files with the keyword snpEff I think I found something that MIGHT be related to this problem:

genome_version:{help:"Genome version for annotating variants using Cravat and SnpEff", choices:["hg19", "hg38"]}

Maybe it's not working because SnpEff only accepts hg19 and hg38? This is just an uneducated guess so I'm not sure.

[brianjohnhaas]

Hi, It looks like the main error is: NoSuchFileException: /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/SRR10075970_read_1.fastq.gz Could it be that the file is located elsewhere? Wrt snpeff, it might be that it's only set up for human. I think you'll need to disable all the annotations. I don't see an interface to doing this from the ctat_mutations script, but there is an 'annotate_variants' boolean value that can be set to false in the WDL/ctat_mutations.wdl, and that should force that whole annotation section of the pipeline to be skipped.

On Fri, Apr 19, 2024 at 4:08 AM cachedpotato ***@***.***> wrote: Thank you for your help! I greatly appreciate it. I'm still encountering problems unfortunately. First, here's the log file

I made.

log.txt It's quite long, but I'll try my best to summarize. At some point I started getting a bunch of this message: ... Key/s [memory, disks, docker, preemptible] is/are not supported by

backend. Unsupported attributes will not be part of job executions.

then I got some error related to SplitIntervals: Job ctat_mutations.SplitIntervals:NA:1 exited with return code 1 which

has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.

After which GATK failed to run and the Workflow transitioned to failed

state.

I'm not a competent coder, nor do I know anything about .wdl files, but

searching through files with the keyword snpEff I think I found something that MIGHT be related to this problem:

genome_version:{help:"Genome version for annotating variants using Cravat

and SnpEff", choices:["hg19", "hg38"]}

Maybe it's not working because SnpEff only accepts hg19 and hg38? This is

just an uneducated guess so I'm not sure.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID:

***@***.***>

…

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

[cachedpotato]

Hello,

it was dumb of me not to properly check the file names. Sorry about that.
I'm still struggling with errors. Long story short, I kind of need to run things using docker atm and I'm not used to creating docker images, which led me through a plethora of problems. My most recent attempt was to create a fork of this repo, change the annotate_variants value and create a new docker image using the Dockerfile in the repo.

creating the image with docker build -t test . (inside the Docker dir) then running it gave me this error:

docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "/usr/local/src/ctat-mutations/ctat-mutations": stat /usr/local/src/ctat-mutations/ctat-mutations: no such file or directory: unknown.

I really wish I could've solved it myself, you've been too kind and I really don't want to waste your time, but I'm really grasping at straws now. Could you give me some insight on how to create this custom docker image?

just in case you're wondering, the only thing I changed from the original git repo are the following:

1. Dockerfile

WORKDIR $SRC
ENV CTAT_MUTATIONS_TAG=v4.1.0
ENV CTAT_MUTATIONS_COMMIT=86fa82a26b1671ebe462ecea097a65e16511ff43
RUN git clone https://github.com/cachedpotato/ctat-mutations-noVA.git && \
    cd ctat-mutations-noVA && \
    git checkout $CTAT_MUTATIONS_COMMIT && \
    git submodule init && git submodule update && \
    git submodule foreach --recursive git submodule init && \
    git submodule foreach --recursive git submodule update && \
    make

(I did not encounter any warnings/errors during the building process if I remember correctly)
2) ctat_mutations.wdl

Boolean annotate_variants = false

Thanks.

p.s If I'm violating any sort of ToS by making a fork I apologize. I'll delete the repo immediately after this is taken care of.

[brianjohnhaas]

Hi, This all looks fine to me, and is definitely the way I'd recommend going about all of this. It's not clear to me why the docker build is giving you trouble, but it could be related to the docker installation. Have you been able to create other docker images there? Like something very simple?

…

On Mon, Apr 22, 2024 at 4:45 AM cachedpotato ***@***.***> wrote: Hello, it was dumb of me not to properly check the file names. Sorry about that. I'm still struggling with errors. Long story short, I kind of need to run things using docker atm and I'm not used to creating docker images, which led me through a plethora of problems. My most recent attempt was to create a fork of this repo, change the annotate_variants value and create a new docker image using the Dockerfile in the repo. creating the image with docker build -t test . (inside the Docker dir) then running it gave me this error: docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "/usr/local/src/ctat-mutations/ctat-mutations": stat /usr/local/src/ctat-mutations/ctat-mutations: no such file or directory: unknown. I really wish I could've solved it myself, you've been too kind and I really don't want to waste your time, but I'm really grasping at straws now. Could you give me some insight on how to create this custom docker image? just in case you're wondering, the only thing I changed from the original git repo are the following: 1. Dockerfile WORKDIR $SRCENV CTAT_MUTATIONS_TAG=v4.1.0ENV CTAT_MUTATIONS_COMMIT=86fa82a26b1671ebe462ecea097a65e16511ff43RUN git clone https://github.com/cachedpotato/ctat-mutations-noVA.git && \ cd ctat-mutations-noVA && \ git checkout $CTAT_MUTATIONS_COMMIT && \ git submodule init && git submodule update && \ git submodule foreach --recursive git submodule init && \ git submodule foreach --recursive git submodule update && \ make (I did not encounter any warnings/errors during the building process if I remember correctly) 2) ctat_mutations.wdl Boolean annotate_variants = false Thanks. p.s If I'm violating any sort of ToS by making a fork I apologize. I'll delete the repo immediately after this is taken care of. — Reply to this email directly, view it on GitHub <#134 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXYS74EJJ5IYKERZV63Y6TEZBAVCNFSM6AAAAABGBLEMQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRYHAZTENZYGE> . You are receiving this because you commented.Message ID: ***@***.***>

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

[cachedpotato]

Hello,

Did take a while but I managed to get the docker container working.

I tried re-configuring a bunch of boolean values, changed the input from fasta to bam, but nothing worked. To my understanding it always fails to make a "valid cross device link" and/or fails at the SplitIntervals stage. Here are the logs:

logChangeAVOnly.txt

logBam2.txt

Do you think there's something else I need to change besides annotate_variants? As I've said I tried changing a bunch of other values (both the ones in the submodule and the ones in ctat-mutations.wdl file, below annotate_variants), but it gave me more errors.

If you can't find anything that's fine, I'll just create a simple pipeline myself if things don't work out again.

Thanks!

[brianjohnhaas]

The cross-device link errors sound familiar... make sure that you're running it where all your resources are located on the same disk (or mount point) and I think that problem should go away. But, definitely worth pursuing the simpler pipeline idea too and avoid these headaches.

…

On Thu, May 2, 2024 at 8:46 PM cachedpotato ***@***.***> wrote: Hello, Did take a while but I managed to get the docker container working. I tried re-configuring a bunch of boolean values, changed the input from fasta to bam, but nothing worked. To my understanding it always fails to make a "valid cross device link" and/or fails at the SplitIntervals stage. Here are the logs: logChangeAVOnly.txt <https://github.com/NCIP/ctat-mutations/files/15195261/logChangeAVOnly.txt> logBam2.txt <https://github.com/NCIP/ctat-mutations/files/15195262/logBam2.txt> Do you think there's something else I need to change besides annotate_variants? As I've said I tried changing a bunch of other values (both the ones in the submodule and the ones in ctat-mutations.wdl file, below annotate_variants), but it gave me more errors. If you can't find anything that's fine, I'll just create a simple pipeline myself if things don't work out again. Thanks! — Reply to this email directly, view it on GitHub <#134 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX7ETB6AUVHKDMKY5ULZALM43AVCNFSM6AAAAABGBLEMQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJRHE3DENBSG4> . You are receiving this because you commented.Message ID: ***@***.***>

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