Localization via hard link has failed:

[vzupan3]

Hi!

I am running CTAT_mutations with docker, but when testing the pipeline with test reads, the Workflow transitions to state Failed. The main warning I get is: Localization via hard link has failed: /data/ctat_mutations_outdir1/cromwell-executions/ctat_mutations/6523153f-d4e1-410a-ac09-6a1adc7e038e/call-VariantFiltration/inputs/-1786084250/ref_genome.dict -> /ctat_genome_lib_build_dir/ref_genome.dict: Invalid cross-device link. I would appreciate any suggestions on how to resolve the issue. Many thanks, Andrej.

[brianjohnhaas]

Hi,

Can you give me the command you're using for this and tell me how you're using docker here? I'll try to reproduce the issue.

best,

~brian

On Mon, Mar 28, 2022 at 11:17 AM vzupan3 @.***> wrote:

Hi!

I am running CTAT_mutations with docker, but when testing the pipeline with test reads, the Workflow transitions to state Failed. The main warning I get is: Localization via hard link has failed: /data/ctat_mutations_outdir1/cromwell-executions/ctat_mutations/6523153f-d4e1-410a-ac09-6a1adc7e038e/call-VariantFiltration/inputs/-1786084250/ref_genome.dict -> /ctat_genome_lib_build_dir/ref_genome.dict: Invalid cross-device link. I would appreciate any suggestions on how to resolve the issue. Many thanks, Andrej.

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[vzupan3]

Hi Brian. Thank you for the reply.

The command would be: andrej@andrej-VirtualBox:~$ sudo docker run --rm -v pwd:/data -v $HOME/ctat_genome_lib_build_dir:/ctat_genome_lib_build_dir:ro trinityctat/ctat_mutations /usr/local/src/ctat-mutations/ctat_mutations --left /data/LibZupan701_S36_R1_001.fastq.gz --right /data/LibZupan701_S36_R2_001.fastq.gz --sample_id test1 --output /data/ctat_mutations_outdir1 --cpu 10 --genome_lib_dir /ctat_genome_lib_build_dir

I just followed the instructions for installation with docker (% docker pull trinityctat/ctat_mutations) with the exception of: "pip install requests open-cravat==2.0.1", where I had to go with special instructions for Ubuntu as described in Open-Cravat guidelines, since pip3 provided by apt does not install executables properly for Ubuntu.

I hope that helps,

Many thanks,

Andrej

[brianjohnhaas]

Thanks for the info!

Do you see that ref_genome.dict file in your ctat genome lib dir? There's some additional setup instructions for populating and configuring the ctat genome lib for use with the ctat mutation pipeline, and I'm wondering if that all happened ok. Generating the .dict file is part of that process, if I remember correctly.

best,

~b

On Tue, Mar 29, 2022 at 10:12 AM vzupan3 @.***> wrote:

Hi Brian. Thank you for the reply.

The command would be: @.***:~$ sudo docker run --rm -v pwd:/data -v $HOME/ctat_genome_lib_build_dir:/ctat_genome_lib_build_dir:ro trinityctat/ctat_mutations /usr/local/src/ctat-mutations/ctat_mutations --left /data/LibZupan701_S36_R1_001.fastq.gz --right /data/LibZupan701_S36_R2_001.fastq.gz --sample_id test1 --output /data/ctat_mutations_outdir1 --cpu 10 --genome_lib_dir /ctat_genome_lib_build_dir

I just followed the instructions for installation with docker (% docker pull trinityctat/ctat_mutations) with the exception of: "pip install requests open-cravat==2.0.1", where I had to go with special instructions for Ubuntu as described in Open-Cravat guidelines, since pip3 provided by apt does not install executables properly for Ubuntu.

I hope that helps,

Many thanks,

Andrej

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/108#issuecomment-1081922930, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX4KRUVP7DMGYJI2T3LVCMFS3ANCNFSM5R3PWUBA . You are receiving this because you commented.Message ID: @.***>

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

[vzupan3]

I just checked and yes, the file ref_genome.dict is in ctat genome lib dir. But interestingly, when searching that file under the output dir its states that: The link ref_genome_dict is broken, because its target /ctat_genome_lib_build_dir/-ref_genome.dict doesn't exist.

I hope that helps,

Andrej

[brianjohnhaas]

Is it really looking for the file /ctat_genome_lib_build_dir/-ref_genome.dict (with a dash) instead of /ctat_genome_lib_build_dir/ref_genome.dict ?

To troubleshoot it further, I'd suggest running docker interactively and checking the contents of the ctat genome lib like so:

docker run --rm -it -v pwd:/data -v $HOME/ctat_genome_lib_build_dir:/ctat_genome_lib_build_dir:ro trinityctat/ctat_mutations bash

then

ls -ltr /ctat_genome_lib_build_dir/

and see that the .dict and other files are showing up ok.

Let's see how that goes.

best,

~b

On Tue, Mar 29, 2022 at 1:13 PM vzupan3 @.***> wrote:

I just checked and yes, the file ref_genome.dict is in ctat genome lib dir. But interestingly, when searching that file under the output dir its states that: The link ref_genome_dict is broken, because its target /ctat_genome_lib_build_dir/-ref_genome.dict doesn't exist.

I hope that helps,

Andrej

— Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/108#issuecomment-1082147978, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX2NQ75A7PK2WRFVQILVCM25DANCNFSM5R3PWUBA . You are receiving this because you commented.Message ID: @.***>

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