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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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Annotate CRAVAT error #126

Open gianfilippo opened 10 months ago

gianfilippo commented 10 months ago

Hi,

I am running the latest version of your pipeline (3.3.1) and it got stuck in a couple of occasions. The most relevant, for the moment, is the Annotate CRAVAT, since cravat is reporting an error related to an erroneous option used (see below).

How can I fix it ?

Thanks

[First 3000 bytes]:+ echo '########### Annotate CRAVAT #############'

CMD: annotate_with_cravat: oc run /home/project/scripts/MC01N/cromwell-executions/ctat_mutations/e9895a07-0b11-4196-9113-83dacb214059/call-AnnotateVariants/annotate_variants_wf/6f770036-3c25-4615-b15e-382002860a9d/call-open_cravat/inputs/559431456/MC01N.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=/home/project/scripts/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t vcf -l hg38 -d -n MC01N.cravat.tmp

brianjohnhaas commented 10 months ago

hi,

Are you using the singularity image? That's the best way to run this, particularly if the cravat version differs from what we have installed in the image.

If needed, you can run with --no_cravat to bypass that step.

On Sat, Sep 9, 2023 at 9:11 PM Gianfilippo Coppola @.***> wrote:

Hi,

I am running the latest version of your pipeline (3.3.1) and it got stuck in a couple of occasions. The most relevant, for the moment, is the Annotate CRAVAT, since cravat is reporting an error related to an erroneous option used (see below).

How can I fix it ?

Thanks

[First 3000 bytes]:+ echo '########### Annotate CRAVAT #############'

- cravat_lib_dir=/home/project/scripts/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat

  • '[' /home/project/scripts/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat == '' ']'
  • export TMPDIR=/tmp
  • TMPDIR=/tmp
  • /home/project/scripts/ctat-mutations-CTAT-Mutations-v3.3.1/src/annotate_with_cravat.py --input_vcf /home/project/scripts/MC01N/cromwell-executions/ctat_mutations/e9895a07-0b11-4196-9113-83dacb214059/call-AnnotateVariants/annotate_variants_wf/6f770036-3c25-4615-b15e-382002860a9d/call-open_cravat/inputs/559431456/MC01N.annot_cosmic.vcf.gz --genome hg38 --cravat_lib_dir /home/project/scripts/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat --output_vcf MC01N.cravat.tmp.vcf usage: oc run [-h] [-a ANNOTATORS [ANNOTATORS ...]] [-e EXCLUDES [EXCLUDES ...]] [-n RUN_NAME] [-d OUTPUT_DIR] [--startat {converter,mapper,annotator,aggregator,postaggregator,reporter}] [--endat {converter,mapper,annotator,aggregator,postaggregator,reporter}] [--skip {converter,mapper,annotator,aggregator,postaggregator,reporter} [{converter,mapper,annotator,aggregator,postaggregator,reporter} ...]] [-c CONF] [--cs CONFS] [-v] [-t {excel,text} [{excel,text} ...]] [-l {hg38,hg19,hg18}] [-x] [--newlog] [--note NOTE] [--mp MP] [-i {cravat,oldcravat,vcf}] [--temp-files] [--writeadmindb] [--jobid JOBID] [--version] [--separatesample] [--primary-transcript [PRIMARY_TRANSCRIPT [PRIMARY_TRANSCRIPT ...]]] [--cleanrun] [--do-not-change-status] [--module-option [MODULE_OPTION [MODULE_OPTION ...]]] [--system-option [SYSTEM_OPTION [SYSTEM_OPTION ...]]] [--silent] [inputs [inputs ...]] oc run: error: argument -t: invalid choice: 'vcf' (choose from 'excel', 'text')

CMD: annotate_with_cravat: oc run /home/project/scripts/MC01N/cromwell-executions/ctat_mutations/e9895a07-0b11-4196-9113-83dacb214059/call-AnnotateVariants/annotate_variants_wf/6f770036-3c25-4615-b15e-382002860a9d/call-open_cravat/inputs/559431456/MC01N.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=/home/project/scripts/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t vcf -l hg38 -d -n MC01N.cravat.tmp

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gianfilippo commented 10 months ago

Hi,

yes, I forgot to mention that I am running the singularity version. I followed the steps described here https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation including Step 4 to install Open-CRAVAT 2.0.1

I should add that I had to also download the github CTAT-Mutations-v3.3.1 source code, since the ctat-mutation-lib-integration.py is missing, otherwise.

I believe the Open-CRAVAT package was missing from the singularity image

brianjohnhaas commented 10 months ago

I see. I'll look into this and see what needs to be modified here. More soon.

On Sat, Sep 9, 2023 at 10:13 PM Gianfilippo Coppola < @.***> wrote:

Hi,

yes, I forgot to mention that I am running the singularity version. I followed the steps described here https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation including Step 4 to install Open-CRAVAT 2.0.1

I should add that I had to also download the github CTAT-Mutations-v3.3.1 source code, since the ctat-mutation-lib-integration.py is missing, otherwise.

I believe the Open-CRAVAT package was missing from the singularity image

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gianfilippo commented 10 months ago

Thanks!

On Sun, Sep 10, 2023 at 9:30 AM Brian Haas @.***> wrote:

I see. I'll look into this and see what needs to be modified here. More soon.

On Sat, Sep 9, 2023 at 10:13 PM Gianfilippo Coppola < @.***> wrote:

Hi,

yes, I forgot to mention that I am running the singularity version. I followed the steps described here https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation including Step 4 to install Open-CRAVAT 2.0.1

I should add that I had to also download the github CTAT-Mutations-v3.3.1 source code, since the ctat-mutation-lib-integration.py is missing, otherwise.

I believe the Open-CRAVAT package was missing from the singularity image

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brianjohnhaas commented 10 months ago

I've updated Step 4 now in the documentation: https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation

I'm testing it out right now... takes some time to run, but I'm hopeful. I'll let you know when it completes.

On Sun, Sep 10, 2023 at 9:36 AM Gianfilippo Coppola < @.***> wrote:

Thanks!

On Sun, Sep 10, 2023 at 9:30 AM Brian Haas @.***> wrote:

I see. I'll look into this and see what needs to be modified here. More soon.

On Sat, Sep 9, 2023 at 10:13 PM Gianfilippo Coppola < @.***> wrote:

Hi,

yes, I forgot to mention that I am running the singularity version. I followed the steps described here

https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation including Step 4 to install Open-CRAVAT 2.0.1

I should add that I had to also download the github CTAT-Mutations-v3.3.1 source code, since the ctat-mutation-lib-integration.py is missing, otherwise.

I believe the Open-CRAVAT package was missing from the singularity image

— Reply to this email directly, view it on GitHub <

https://github.com/NCIP/ctat-mutations/issues/126#issuecomment-1712687386>,

or unsubscribe <

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brianjohnhaas commented 10 months ago

ok, looks like it's working now.

I edited the documentation again.

Basically, use the open cravat that's already installed in the singularity image.

Download the additional cravat library as now indicated in the documentation and unpack it in your ctat_genome_lib/ctat_mutation_lib/ subdirectory.

Then, run the singularity command again as you did before. It should pick up where it left off hopefully and finish up.

Let me know if it gives you any trouble.

Overall, the installation is now easier than before, but does require that you download some large file instead of having cravat do it. Probably better this way now tbh.

best,

~b

On Sun, Sep 10, 2023 at 10:24 AM Brian Haas @.***> wrote:

I've updated Step 4 now in the documentation: https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation

I'm testing it out right now... takes some time to run, but I'm hopeful. I'll let you know when it completes.

On Sun, Sep 10, 2023 at 9:36 AM Gianfilippo Coppola < @.***> wrote:

Thanks!

On Sun, Sep 10, 2023 at 9:30 AM Brian Haas @.***> wrote:

I see. I'll look into this and see what needs to be modified here. More soon.

On Sat, Sep 9, 2023 at 10:13 PM Gianfilippo Coppola < @.***> wrote:

Hi,

yes, I forgot to mention that I am running the singularity version. I followed the steps described here

https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation including Step 4 to install Open-CRAVAT 2.0.1

I should add that I had to also download the github CTAT-Mutations-v3.3.1 source code, since the ctat-mutation-lib-integration.py is missing, otherwise.

I believe the Open-CRAVAT package was missing from the singularity image

— Reply to this email directly, view it on GitHub <

https://github.com/NCIP/ctat-mutations/issues/126#issuecomment-1712687386>,

or unsubscribe <

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gianfilippo commented 10 months ago

Hi,

thanks for updating the documentation.

Unfortunately, I still get the error. Just to clarify, I did not install open-cravat directly onto the system, rather I created a conda environment for it. I reran the pipeline using the provided test FASTQ files, without activating the open-cravat, to make sure it would run the provided version. Still, I get the same error

oc run: error: argument -t: invalid choice: 'vcf' (choose from 'excel', 'text')

I then edited the annotate_with_cravat.py under. ctat-mutations-CTAT-Mutations-v3.3.1/src and replaced 'vcf' with 'text' under the '-t' option. Now the open-cravat did not produce any error, but the following step fails (see below)

CMD: annotate_with_cravat: oc run /home/project/scripts/MC01N/cromwell-executions/ctat_mutations/da88d4de-483f-4832-a617-3d6ce8c742df/call-AnnotateVariants/annotate_variants_wf/dd4ace68-921a-484f-a695-37bb85cb5fb1/call-open_cravat/inputs/747081951/MC01N.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=/home/project/scripts/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t text -l hg38 -d -n MC01N.cravat.tmp

[2023-09-10 17:24:35,55] [info] WorkflowManagerActor WorkflowActor-da88d4de-483f-4832-a617-3d6ce8c742df is in a terminal state: WorkflowFailedState

brianjohnhaas commented 10 months ago

Hi,

The cravat in the singularity image shouldn't require any change to the usage.

If you want to test it out with the small data set that comes with the ctat-mutations pipeline, under

ctat-mutations/testing/

you can run

make HC_standard_singularity

it does require that you have the singularity image set up as: ../Docker/ctat_mutations.vLATEST.simg

from the testing directory.

It should run end-to-end under an hour, including cravat.

Again, no changes to the way cravat is run should be needed for a successful execution here.

If needed, you could replace your ctat_mutations_lib/cravat/ contents with what we now provide according to the updated installation guide (step 4).

Hope this helps,

~b

On Sun, Sep 10, 2023 at 1:50 PM Gianfilippo Coppola < @.***> wrote:

Hi,

thanks for updating the documentation.

Unfortunately, I still get the error. Just to clarify, I did not install open-cravat directly onto the system, rather I created a conda environment for it. I reran the pipeline without activating the open-cravat, to make sure it would run the provided version. Still, I get the same error

oc run: error: argument -t: invalid choice: 'vcf' (choose from 'excel', 'text')

I then edited the annotate_with_cravat.py under. ctat-mutations-CTAT-Mutations-v3.3.1/src and replaced 'vcf' with 'text' under the '-t' option. Now the open-cravat did not produce any error, but the following step fails (see below)

CMD: annotate_with_cravat: oc run /home/project/scripts/MC01N/cromwell-executions/ctat_mutations/da88d4de-483f-4832-a617-3d6ce8c742df/call-AnnotateVariants/annotate_variants_wf/dd4ace68-921a-484f-a695-37bb85cb5fb1/call-open_cravat/inputs/747081951/MC01N.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=/home/project/scripts/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t text -l hg38 -d -n MC01N.cravat.tmp

/home/project/scripts/ctat-mutations-CTAT-Mutations-v3.3.1/src/groom_vcf.py MC01N.cravat.tmp.vcf MC01N.cravat.groom.vcf Traceback (most recent call last): File "/home/project/scripts/ctat-mutations-CTAT-Mutations-v3.3.1/src/groom_vcf.py", line 43, in with ctat_util.open_file_for_reading(args.str_input_file) as hndl_vcf: File "/home/project/scripts/ctat-mutations-CTAT-Mutations-v3.3.1/src/ctat_util.py", line 10, in open_file_for_reading return open(filename, 'rt', encoding="utf-8", errors='ignore') # regular text file FileNotFoundError: [Errno 2] No such file or directory: 'MC01N.cravat.tmp.vcf'

[2023-09-10 17:24:35,55] [info] WorkflowManagerActor WorkflowActor-da88d4de-483f-4832-a617-3d6ce8c742df is in a terminal state: WorkflowFailedState

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gianfilippo commented 10 months ago

Hi,

I just ran the "make HC_standard_singularity" command under testing and got the same error. Somehow it is running a version of open-cravat that does not support the "vcf" entri for the "-t" option.

I will probably try the manual install, since Docker does not run on my cluster.

Can you please let me know what version of numpy you packaged with the singularity image file ?

Thanks

brianjohnhaas commented 10 months ago

That is incredibly strange. Here's what's in the image:

singularity shell -e ctat_mutations.vLATEST.simg

Singularity> pip list | grep numpy

numpy 1.21.6

Singularity> oc version

2.0.1

Singularity> which oc

/opt/conda/bin/oc

The singularity image is based on the docker image, and the Dockerfile is here:

https://github.com/NCIP/ctat-mutations/blob/master/Docker/Dockerfile

Maybe it's reconfiguring some settings based on your home environment. You can try adding -H /tmp to the singularity exec and see if that helps, including double checking which 'oc' is being used here - ensuring it's the one in the image.

best,

~b

On Mon, Sep 11, 2023 at 12:39 AM Gianfilippo Coppola < @.***> wrote:

Hi,

I just ran the "make HC_standard_singularity" command under testing and got the same error. Somehow it is running a version of open-cravat that does not support the "vcf" entri for the "-t" option.

I will probably try the manual install, since Docker does not run on my cluster.

Can you please let me know what version of numpy you packaged with the singularity image file ?

Thanks

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gianfilippo commented 10 months ago

Hi,

I did some more tests and reinstalled open-cravat 2.0.1 under a conda env CTAT I created. I can run oc and the version is confirmed to be 2.0.1 oc run --version 2.0.1

I then ran the oc CMD directly (from the log file reporting the error) oc run MC01N/cromwell-executions/ctat_mutations/785846d3-5ab1-4930-9b61-cff25eead75f/call-AnnotateVariants/annotate_variants_wf/8a9fc0bb-6c99-4320-a995-4c7522549aeb/call-open_cravat/inputs/-1303126155/MC01N.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t vcf -l hg38 -d -n MC01N.cravat.tmp

I still get the error: argument -t: invalid choice: 'vcf (see below). usage: oc run [-h] [-a ANNOTATORS [ANNOTATORS ...]] [-e EXCLUDES [EXCLUDES ...]] [-n RUN_NAME] [-d OUTPUT_DIR] [--startat {converter,mapper,annotator,aggregator,postaggregator,reporter}] [--endat {converter,mapper,annotator,aggregator,postaggregator,reporter}] [--skip {converter,mapper,annotator,aggregator,postaggregator,reporter} [{converter,mapper,annotator,aggregator,postaggregator,reporter} ...]] [-c CONF] [--cs CONFS] [-v] [-t {text,excel} [{text,excel} ...]] [-l {hg38,hg19,hg18}] [-x] [--newlog] [--note NOTE] [--mp MP] [-i {cravat,oldcravat,vcf}] [--temp-files] [--writeadmindb] [--jobid JOBID] [--version] [--separatesample] [--primary-transcript [PRIMARY_TRANSCRIPT [PRIMARY_TRANSCRIPT ...]]] [--cleanrun] [--do-not-change-status] [--module-option [MODULE_OPTION [MODULE_OPTION ...]]] [--system-option [SYSTEM_OPTION [SYSTEM_OPTION ...]]] [--silent] [inputs [inputs ...]] oc run: error: argument -t: invalid choice: 'vcf' (choose from 'text', 'excel')

I am a little lost at this point.....

brianjohnhaas commented 10 months ago

Yes, I figured it out just recently. I think they updated 2.0.1 after I had installed it into the docker. If you install 2.1.0 instead, I think you should be fine.

Note, I just posted a new release including new docker and singularity images, and these now use the v2.1.0.

hope this helps,

~b

On Tue, Sep 19, 2023 at 3:54 PM Gianfilippo Coppola < @.***> wrote:

Hi,

I did some more tests and reinstalled open-cravat 2.0.1 under a conda env CTAT I created. I can run oc and the version is confirmed to be 2.0.1 oc run --version 2.0.1

I then ran the oc CMD directly (from the log file reporting the error) oc run MC01N/cromwell-executions/ctat_mutations/785846d3-5ab1-4930-9b61-cff25eead75f/call-AnnotateVariants/annotate_variants_wf/8a9fc0bb-6c99-4320-a995-4c7522549aeb/call-open_cravat/inputs/-1303126155/MC01N.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t vcf -l hg38 -d -n MC01N.cravat.tmp

I still get the error: argument -t: invalid choice: 'vcf (see below). usage: oc run [-h] [-a ANNOTATORS [ANNOTATORS ...]] [-e EXCLUDES [EXCLUDES ...]] [-n RUN_NAME] [-d OUTPUT_DIR] [--startat {converter,mapper,annotator,aggregator,postaggregator,reporter}] [--endat {converter,mapper,annotator,aggregator,postaggregator,reporter}] [--skip {converter,mapper,annotator,aggregator,postaggregator,reporter} [{converter,mapper,annotator,aggregator,postaggregator,reporter} ...]] [-c CONF] [--cs CONFS] [-v] [-t {text,excel} [{text,excel} ...]] [-l {hg38,hg19,hg18}] [-x] [--newlog] [--note NOTE] [--mp MP] [-i {cravat,oldcravat,vcf}] [--temp-files] [--writeadmindb] [--jobid JOBID] [--version] [--separatesample] [--primary-transcript [PRIMARY_TRANSCRIPT [PRIMARY_TRANSCRIPT ...]]] [--cleanrun] [--do-not-change-status] [--module-option [MODULE_OPTION [MODULE_OPTION ...]]] [--system-option [SYSTEM_OPTION [SYSTEM_OPTION ...]]] [--silent] [inputs [inputs ...]] oc run: error: argument -t: invalid choice: 'vcf' (choose from 'text', 'excel')

I am a little lost at this point.....

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gianfilippo commented 10 months ago

Hi,

I am sorry, but I am getting the same error "oc run: error: argument -t: invalid choice: 'vcf' (choose from 'text', 'excel')"

I also tried by manually entering the command.

The oc version is 2.1.0 and the "-t" input format is the same as the latest version, so probably you wrote the script for a version earlier than 2.0.1, since that did not work either for me.

Can you not update the python script to use the newer input to the -t argument ?

Best

gianfilippo commented 10 months ago

I installed oc version 2.0.0 and the -t argument input is probably consistent with your script.

brianjohnhaas commented 10 months ago

I wish I had more info to help. I didn't write any custom scripts here... it just runs 'oc' from the v 2.1.0 version. I've run it within the docker, a singularity image, and natively on my ubuntu VM.

Here's the dockerfile used for the docker and singularity images, and points out the version I'm using here for the latest release: https://github.com/NCIP/ctat-mutations/blob/f99e73cbb7911bffe2b303e94d59121b92d48b73/Docker/Dockerfile#L54

On Tue, Sep 19, 2023 at 6:44 PM Gianfilippo Coppola < @.***> wrote:

Hi,

I am sorry, but I am getting the same error "oc run: error: argument -t: invalid choice: 'vcf' (choose from 'text', 'excel')"

I also tried by manually entering the command.

The oc version is 2.1.0 and the "-t" input format is the same as the latest version, so probably you wrote the script for a version earlier than 2.0.1, since that did not work either for me.

Can you not update the python script to use the newer input to the -t argument ?

Best

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gianfilippo commented 10 months ago

I am really referring to the annotate_with_cravat.py script, under ctat-mutations-v4.0.0/src/ In there you define the oc input arguments, including "-t". Can you not package the singularity image with oc 2.0.0 ?

brianjohnhaas commented 10 months ago

it needs to be parameterized as it is. I'm sorry if it's not working for you - it's entirely unclear as to why this is the case. Feel free to take the code and modify it to your needs, or explore other options.

On Tue, Sep 19, 2023 at 9:29 PM Gianfilippo Coppola < @.***> wrote:

I am really referring to the annotate_with_cravat.py script, under ctat-mutations-v4.0.0/src/ In there you define the oc input arguments, including "-t". Can you not package the singularity image with oc 2.0.0 ?

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gianfilippo commented 10 months ago

I understand. Thanks anyway for your help!

On Tue, Sep 19, 2023 at 9:38 PM Brian Haas @.***> wrote:

it needs to be parameterized as it is. I'm sorry if it's not working for you - it's entirely unclear as to why this is the case. Feel free to take the code and modify it to your needs, or explore other options.

On Tue, Sep 19, 2023 at 9:29 PM Gianfilippo Coppola < @.***> wrote:

I am really referring to the annotate_with_cravat.py script, under ctat-mutations-v4.0.0/src/ In there you define the oc input arguments, including "-t". Can you not package the singularity image with oc 2.0.0 ?

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