questions about some commands #17
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Let me try with a separate user because I am normally a sudo user on the
system so didn't realize this.
You may be able to do --writable-tmpfs instead of overlay. I will check in
the morning though to be sure.
…On Thu, Apr 11, 2024, 9:21 PM spoonbender76 ***@***.***> wrote:
I am trying the new big singularity image and from the document
1. --overlay $(pwd)/tempdir will trigger
FATAL:container creation failed:while setting overlay session layout: only
root user can use sandbox overlay in setuid mode
still require root for singularity users
2. Even with -w miniprot It shows
chosen protein algos: None
And I don't know this error can be ignored or have any affects.
WARN: Unknown directive runOptions for process pasa
[b7/9cbcde] NOTE: Process pasa(1) terminated with an error exit status(2)
- - Error is ignored
image.png (view on web)
<https://github.com/formbio/FLAG/assets/109210499/0062f413-7ee7-443e-996b-4565662c3cde>
#If Liftoff is desired the above command can be modified such as below:
singularity run --bind $(pwd):/data --bind $(pwd)/tempdir:/tmp \
--overlay $(pwd)/tempdir singularity_flag.image \
-g Erynnis_tages-GCA_905147235.1-softmasked.fa -r curatedButterflyRNA.fa \
-p curatedButterflyProteins.fa -f GCF_009731565.1_Dplex_v4_genomic.fa \
-a GCF_009731565.1_Dplex_v4_genomic.gff -m skip -t true \
-l lepidoptera_odb10 \
-z Helixer,helixer_trained_augustus -q vertebrate -s small -n Eynnis_tages \
-w miniprot -y normal -p singularity -o outputdir -u singularity
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Pasa is failing because it's trying to write a sqlite file is my guess
related to the overlay. The warning you have for it is fine.
Even if it does fail you should get good results since Splign will also do
transcript to genome alignments but it's slightly better with Pasa working.
…On Thu, Apr 11, 2024, 10:44 PM William Troy ***@***.***> wrote:
Let me try with a separate user because I am normally a sudo user on the
system so didn't realize this.
You may be able to do --writable-tmpfs instead of overlay. I will check
in the morning though to be sure.
On Thu, Apr 11, 2024, 9:21 PM spoonbender76 ***@***.***>
wrote:
> I am trying the new big singularity image and from the document
>
> 1. --overlay $(pwd)/tempdir will trigger
>
> FATAL:container creation failed:while setting overlay session layout:
> only root user can use sandbox overlay in setuid mode
>
> still require root for singularity users
>
> 2. Even with -w miniprot It shows
>
> chosen protein algos: None
>
> And I don't know this error can be ignored or have any affects.
>
> WARN: Unknown directive runOptions for process pasa
> [b7/9cbcde] NOTE: Process pasa(1) terminated with an error exit
> status(2) - - Error is ignored
>
> image.png (view on web)
> <https://github.com/formbio/FLAG/assets/109210499/0062f413-7ee7-443e-996b-4565662c3cde>
>
> #If Liftoff is desired the above command can be modified such as below:
>
> singularity run --bind $(pwd):/data --bind $(pwd)/tempdir:/tmp \
> --overlay $(pwd)/tempdir singularity_flag.image \
> -g Erynnis_tages-GCA_905147235.1-softmasked.fa -r curatedButterflyRNA.fa \
> -p curatedButterflyProteins.fa -f GCF_009731565.1_Dplex_v4_genomic.fa \
> -a GCF_009731565.1_Dplex_v4_genomic.gff -m skip -t true \
> -l lepidoptera_odb10 \
> -z Helixer,helixer_trained_augustus -q vertebrate -s small -n Eynnis_tages \
> -w miniprot -y normal -p singularity -o outputdir -u singularity
>
> —
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the protein algo has been fixed as well as instructions for singularity with liftoff. That was a typo thank you for catching those! |
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I setup Docker according to instructions and I've been running Docker example for over 15 hours, but I don't see any signs of it running. There are no splign/augustus processes visible. I have to CTRL-C since it appears to be stalled. By the way, the flags If Liftoff is desired the above command can be modified such as below: nextflow run main.nf -w workdir/ --output outputdir/ nextflow run main.nf -w workdir/ --output outputdir/ |
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This one is interesting. It looks like Splign is stalled out. This is not usually a process that runs into issues so very unsure why it's stalled. If you have the process logs for that one feel free to send it. Augustus and all of the rest of the processes are waiting for Splign to finish before they run as the Splign outputs go into the next processes. And thank you for noticing this I will fix it ASAP. Currently working on making the singularity all run from one large container. |
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Thank you for the quick reply! I ran the docker liftoff example again, but nextflow keeps printing lines to I've attached some log files here for reference. Please let me know if you need any other information. |
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I updated the ncbiclibraries container that splign runs on to hopefully fix the problem you are having. Tested on a completely fresh Debian system that I just installed nextflow and docker on and it ran fine: So id try repulling the containers, specifically ghcr.io/formbio/flag_ncbiclibraries:latest and rerunning and fingers crossed it works. The docker should be much more stable than singularity. |
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I haven't used FLAG in a while, but have you tried running it with the |
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Ya I have. I will do a run tomorrow and add a screenshot to the docs. |
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A screenshot of it working has been added to the readme.md file on the GitHub main branch. This should also help users for reference |
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Details: However, the folder /etc/apptainer/ didn't exist. So, I installed Apptainer v1.31 manually, repulled all containers, and reran the pipeline. Unfortunately, it got stuck at the CombineAndFilter step. Upon closer inspection, I found that this was primarily due to my very slow connection, which took hours to download a BUSCO file |
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Thanks for the update! I'm glad it ran for you!
As for the offline mode that's actually a pretty smart idea. I always have
fast connection so never experienced this issue but an offline mode is
something that should be useful to others. I will put this on my todo list!
…On Mon, May 20, 2024, 8:56 PM spoonbender76 ***@***.***> wrote:
image.png (view on web)
<https://github.com/formbio/FLAG/assets/109210499/c2badc9b-1deb-49af-830a-c03b4073020d>
Thank you for the help! I have completed a FLAG run using Apptainer, but I
encountered significant delays due to the time spent downloading BUSCO
lineage files, likely caused by my connection issues. Is there a way to
specify a local directory for pre-downloaded BUSCO lineage files, and use
the --offline option for all BUSCO commands within the FLAG pipeline?
Details:
I tried to create a FLAG environment with Apptainer using the following
commands:
conda create -n flag apptainer
conda activate flag
cp /etc/apptainer/apptainer.config $CONDA_PREFIX/etc/apptainer/
However, the folder /etc/apptainer/ didn't exist. So, I installed
Apptainer v1.31 manually, repulled all containers, and reran the pipeline.
Unfortunately, it got stuck at the CombineAndFilter step. Upon closer
inspection, I found that this was primarily due to my very slow connection,
which took hours to download a BUSCO file lepidoptera_odb10.tar.gz. I
experienced the same issue with Docker. So I wonder if it's possible to use
--offline option for all BUSCO commands within the FLAG pipeline.
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I am trying the new big singularity image(81.5 G) and from the document I have questions about some commands.
still require root for singularity users. Is this necessary?
And I don't know if this error can be ignored or it has any affects.
-zif Liftoff is desired?In document it says:
If Liftoff is desired the above command can be modified such as below:
In
chosen annotation algothe Liftoff is absent.The text was updated successfully, but these errors were encountered: